From 3bad82850b3ae1cad2d6251e7dbc062be219f109 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Wed, 27 Nov 2024 11:45:00 -0600 Subject: [PATCH 01/15] Blood specimen hierarchy --- src/ontology/modules/specimens.owl | 18 +++++++++--------- src/ontology/templates/specimens.tsv | 18 +++++++++--------- 2 files changed, 18 insertions(+), 18 deletions(-) diff --git a/src/ontology/modules/specimens.owl b/src/ontology/modules/specimens.owl index 75682009..68e3072a 100644 --- a/src/ontology/modules/specimens.owl +++ b/src/ontology/modules/specimens.owl @@ -4263,7 +4263,7 @@ - + @@ -4657,7 +4657,7 @@ - + @@ -4690,7 +4690,7 @@ - + @@ -4727,7 +4727,7 @@ - + @@ -4758,7 +4758,7 @@ - + @@ -5857,7 +5857,7 @@ - + @@ -5893,7 +5893,7 @@ - + @@ -5929,7 +5929,7 @@ - + @@ -5965,7 +5965,7 @@ - + diff --git a/src/ontology/templates/specimens.tsv b/src/ontology/templates/specimens.tsv index 28cc0148..f62d4939 100644 --- a/src/ontology/templates/specimens.tsv +++ b/src/ontology/templates/specimens.tsv @@ -106,7 +106,7 @@ OBI:0002612 fecal swab specimen ready for release stool swab specimen A specime OBI:0002613 environmental swab specimen ready for release A specimen that is collected with a swab from the surface of an environmenal material. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen collecting specimen with swab environmental material ENVO_00010483 OBI:0002627 ribosomal RNA-depleted RNA extract ribosomal RNA-depleted RNA extract pending final vetting An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species). https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1 Looking at the reads for each ribosomal RNA-depleted RNA extract, the vast majority align to protein coding genes based on the ENSEMBL annotation. Dan Berrios subclass RNA extract OBI:0002648 individual organism specimen A specimen composed of an individual organism to be studied in an investigation. EFO_0000542 individual Person: Jie Zheng https://github.com/obi-ontology/obi/issues/1092 equivalent specimen 'has component' exactly 1 'organism' -OBI:0002691 arthropod meal of blood specimen metadata complete blood meal A specimen of the blood ingested by an arthropod. VEuPathDB A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito. Chris Stoeckert|Jie Zheng The mosquito feeds on a human for example, ingests the blood of the human, this blood is then taken from the tummy of a mosquito and a PCR may be run on this specimen to identify that the mosquito definitely fed on a human. VEuPathDB https://github.com/obi-ontology/obi/issues/1117 subclass specimen from organism collecting specimen from organism +OBI:0002691 arthropod meal of blood specimen metadata complete blood meal A specimen of the blood ingested by an arthropod. VEuPathDB A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito. Chris Stoeckert|Jie Zheng The mosquito feeds on a human for example, ingests the blood of the human, this blood is then taken from the tummy of a mosquito and a PCR may be run on this specimen to identify that the mosquito definitely fed on a human. VEuPathDB https://github.com/obi-ontology/obi/issues/1117 subclass blood specimen collecting specimen from organism OBI:0002746 induced sputum specimen A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. PMC3297553 John Judkins subclass specimen from organism collecting specimen from organism sputum UBERON_0007311 OBI:0002774 platelet-poor plasma specimen A blood plasma specimen that is the output of some platelet-poor plasma preparation and is the portion of plasma that contains fewer than 10,000 platelets per microliter. PERSON: Matthew Diller subclass blood plasma specimen OBI:0002778 tracheal aspirate specimen tracheal wash specimen A specimen that is collected with a suctioning tube from the trachea. PMID:25338241 Asiyah Yu Lin ORCID:0000-0003-2620-0345 subclass specimen from organism aspiration specimen collection trachea UBERON_0003126 @@ -118,10 +118,10 @@ OBI:0002783 lower respiratory tract specimen A specimen that is derived from OBI:0002784 anterior nasal swab specimen A specimen that is derived from the anterior nasal wall Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent specimen from organism collecting specimen with swab anterior nasal wall UBERON_3000016 OBI:0002971 endotracheal tube specimen A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea. https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 John Judkins ORCID:0000-0001-6595-0902 subclass specimen from organism collecting specimen from organism respiratory system fluid/secretion UBERON_0006538 OBI:0002972 endotracheal aspirate specimen A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube. https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 John Judkins ORCID:0000-0001-6595-0902 subclass specimen from organism collecting specimen from organism respiratory system fluid/secretion UBERON_0006538 -OBI:0003054 blood specimen in vacutainer Vacutainer sample A blood specimen that is located in a vacutainer. VEuPathDB John Judkins specimen from organism collecting specimen from organism blood UBERON_0000178 -OBI:0003055 blood specimen on filter paper Filter paper sample A blood specimen that is located on a filter paper. Penn Group Jie Zheng|Chris Stoeckert specimen from organism collecting specimen from organism blood UBERON_0000178 -OBI:0003380 placental blood specimen A specimen that is derived from placental blood. VEuPathDB John Judkins equivalent specimen from organism collecting specimen from organism placental blood UBERON_8470000 -OBI:0003415 peripheral blood mononuclear cell specimen PBMC specimen A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system. http://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell Jie Zheng|Chris Stoeckert subclass specimen from organism collecting specimen from organism peripheral blood mononuclear cell CL_2000001 +OBI:0003054 blood specimen in vacutainer Vacutainer sample A blood specimen that is located in a vacutainer. VEuPathDB John Judkins subclass blood specimen collecting specimen from organism blood UBERON_0000178 +OBI:0003055 blood specimen on filter paper Filter paper sample A blood specimen that is located on a filter paper. Penn Group Jie Zheng|Chris Stoeckert subclass blood specimen collecting specimen from organism blood UBERON_0000178 +OBI:0003380 placental blood specimen A specimen that is derived from placental blood. VEuPathDB John Judkins equivalent blood specimen collecting specimen from organism placental blood UBERON_8470000 +OBI:0003415 peripheral blood mononuclear cell specimen PBMC specimen A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system. http://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell Jie Zheng|Chris Stoeckert subclass blood specimen collecting specimen from organism peripheral blood mononuclear cell CL_2000001 OBI:0003482 lymph specimen A specimen that is derived from a portion of lymph collected from an organism. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 specimen from organism collecting specimen from organism (tissue and ('part of' some lymph)) UBERON_0002391 OBI:0003483 digestive tract specimen A specimen that is derived from part of a digestive tract. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 specimen from organism collecting specimen from organism (tissue and ('part of' some 'digestive tract')) UBERON_0001555 OBI:0003595 nasal lavage fluid A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space. Sebastian Duesing|Randi Vita equivalent lavage fluid specimen lavage nasal cavity mucosa UBERON_0001826 @@ -148,10 +148,10 @@ OBI:2000008 semen specimen A specimen that is derived from some semen Mark A. OBI:2000009 bodily fluid specimen A specimen that is derived from some bodily fluid Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism bodily fluid UBERON_0006314 OBI:2000010 chorionic villus specimen A specimen that is derived from some chorionic villus Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'chorionic villus')) UBERON_0007106 OBI:2000011 meconium specimen A specimen that is derived from some meconium Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism meconium UBERON_0007109 -OBI:2000012 umbilical cord blood specimen A specimen that is derived from some umbilical cord blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism umbilical cord blood UBERON_0012168 -OBI:2000013 arterial blood specimen A specimen that is derived from some arterial blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism arterial blood UBERON_0013755 -OBI:2000014 venous blood specimen A specimen that is derived from some venous blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism venous blood UBERON_0013756 -OBI:2000015 capillary blood specimen A specimen that is derived from some capillary blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism capillary blood UBERON_0013757 +OBI:2000012 umbilical cord blood specimen A specimen that is derived from some umbilical cord blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent blood specimen collecting specimen from organism umbilical cord blood UBERON_0012168 +OBI:2000013 arterial blood specimen A specimen that is derived from some arterial blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent blood specimen collecting specimen from organism arterial blood UBERON_0013755 +OBI:2000014 venous blood specimen A specimen that is derived from some venous blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent blood specimen collecting specimen from organism venous blood UBERON_0013756 +OBI:2000015 capillary blood specimen A specimen that is derived from some capillary blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent blood specimen collecting specimen from organism capillary blood UBERON_0013757 OBI:2000016 erythrocyte specimen A specimen that is derived from some erythrocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X subclass specimen from organism collecting specimen with swab erythrocyte CL_0000232 OBI:2000017 reticulocyte specimen A specimen that is derived from some reticulocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X subclass specimen from organism collecting specimen with swab reticulocyte CL_0000558 OBI:2000018 leukocyte specimen A specimen that is derived from some leukocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X subclass specimen from organism collecting specimen with swab leukocyte CL_0000738 From 49fe8b1811c8746cd98d0af5796736dbb1673021 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Wed, 27 Nov 2024 11:50:45 -0600 Subject: [PATCH 02/15] Obsolete duplicate upper respiratory specimen --- src/ontology/modules/obsolete.owl | 15 ++++++++++++ src/ontology/modules/specimens.owl | 36 ---------------------------- src/ontology/templates/obsolete.tsv | 1 + src/ontology/templates/specimens.tsv | 1 - 4 files changed, 16 insertions(+), 37 deletions(-) diff --git a/src/ontology/modules/obsolete.owl b/src/ontology/modules/obsolete.owl index 3aeb9954..f78b9ac0 100644 --- a/src/ontology/modules/obsolete.owl +++ b/src/ontology/modules/obsolete.owl @@ -881,6 +881,21 @@ + + + + + A specimen that is derived from the upper respiratory tract + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + + + obsolete_upper respiratory specimen + true + + + + diff --git a/src/ontology/modules/specimens.owl b/src/ontology/modules/specimens.owl index 68e3072a..a6b28922 100644 --- a/src/ontology/modules/specimens.owl +++ b/src/ontology/modules/specimens.owl @@ -4480,42 +4480,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from the upper respiratory tract - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - upper respiratory specimen - - - - diff --git a/src/ontology/templates/obsolete.tsv b/src/ontology/templates/obsolete.tsv index 39f14605..54c454a5 100755 --- a/src/ontology/templates/obsolete.tsv +++ b/src/ontology/templates/obsolete.tsv @@ -51,6 +51,7 @@ OBI:0001611 obsolete purified MHC direct binding assay ready for release purif OBI:0001712 obsolete B cell epitope direct binding assay ready for release direct binding assay A direct binding assay using a assay IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters subclass Obsolete Class true IAO:0000103 OBI:0001715 obsolete B cell epitope competitive binding assay ready for release competitive binding assay A competitive inhibition of binding assay using a assay IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters subclass Obsolete Class true IAO:0000103 OBI:0001737 obsolete B cell epitope specific X-ray crystallography assay ready for release X-ray crystallography [Ã…] A X-ray crystallography assay measuring epitope specfic antibody binding event in angstroms IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters subclass Obsolete Class true IAO:0000227 OBI:0001738 +OBI:0002782 obsolete_upper respiratory specimen A specimen that is derived from the upper respiratory tract Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 subclass Obsolete Class true IAO:0000227 OBI:2000006 OBI:0100015 obsolete_anatomical entity organizational term An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue' MO Tissue, organ, system, sperm, blood or body location (arm). Bjoern Peters|Philippe Rocca-Serra|Tina Boussard subclass Obsolete Class true IAO:0000228 OBI:0100035 obsolete_immortal cell metadata complete a cell derived from a multicellular organism that has the potential to replicate indefinitely GROUP: OBI Biomaterial Branch a single Hela cell PERSON: Bjoern Peters subclass Obsolete Class true IAO:0000228 OBI:0100039 obsolete_fragment derived from protein metadata incomplete A material entity which is derived from a protein GROUP: IEDB the peptide with sequence SIINFEKL, which is eluted from a cell expressing hen egg lysozyme PERSON: Bjoern Peters subclass Obsolete Class true IAO:0000103 diff --git a/src/ontology/templates/specimens.tsv b/src/ontology/templates/specimens.tsv index f62d4939..25fd252e 100644 --- a/src/ontology/templates/specimens.tsv +++ b/src/ontology/templates/specimens.tsv @@ -113,7 +113,6 @@ OBI:0002778 tracheal aspirate specimen tracheal wash specimen A specimen that OBI:0002779 mid-turbinate nasal swab specimen A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity. https://seattlechildrenslab.testcatalog.org/catalogs/185/files/11633 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent specimen from organism collecting specimen with swab middle nasal concha UBERON_0005921 OBI:0002780 nasal aspirate specimen nasal wash specimen|nasopharyngeal aspirate A specimen that is collected with a suctioning tube from the nasal cavity. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent specimen from organism aspiration specimen collection nasal cavity mucosa UBERON_0001826 OBI:0002781 lower respiratory tract aspirate specimen lower respiratory tract wash specimen A specimen that is collected with a suctioning tube from the lower respiratory tract. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent specimen from organism aspiration specimen collection lower respiratory tract UBERON_0001558 -OBI:0002782 upper respiratory specimen A specimen that is derived from the upper respiratory tract Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent specimen from organism collecting specimen with swab upper respiratory tract UBERON_0001557 OBI:0002783 lower respiratory tract specimen A specimen that is derived from the lower respiratory tract. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent specimen from organism lower respiratory tract UBERON_0001558 OBI:0002784 anterior nasal swab specimen A specimen that is derived from the anterior nasal wall Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent specimen from organism collecting specimen with swab anterior nasal wall UBERON_3000016 OBI:0002971 endotracheal tube specimen A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea. https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 John Judkins ORCID:0000-0001-6595-0902 subclass specimen from organism collecting specimen from organism respiratory system fluid/secretion UBERON_0006538 From bb64dbf29cf39adcb1d60d87d075cd153adcd384 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Wed, 27 Nov 2024 13:27:34 -0600 Subject: [PATCH 03/15] Respiratory system specimen hierarchy --- src/ontology/modules/specimens.owl | 30 ++++++++++++++-------------- src/ontology/templates/specimens.tsv | 30 ++++++++++++++-------------- 2 files changed, 30 insertions(+), 30 deletions(-) diff --git a/src/ontology/modules/specimens.owl b/src/ontology/modules/specimens.owl index a6b28922..d8f1aa2a 100644 --- a/src/ontology/modules/specimens.owl +++ b/src/ontology/modules/specimens.owl @@ -755,7 +755,7 @@ - + @@ -799,7 +799,7 @@ - + @@ -2807,7 +2807,7 @@ - + @@ -3924,7 +3924,7 @@ - + @@ -3998,7 +3998,7 @@ - + @@ -4337,7 +4337,7 @@ - + @@ -4375,7 +4375,7 @@ - + @@ -4411,7 +4411,7 @@ - + @@ -4449,7 +4449,7 @@ - + @@ -4486,7 +4486,7 @@ - + @@ -4518,7 +4518,7 @@ - + @@ -4557,7 +4557,7 @@ - + @@ -4589,7 +4589,7 @@ - + @@ -5575,7 +5575,7 @@ - + @@ -5621,7 +5621,7 @@ - + diff --git a/src/ontology/templates/specimens.tsv b/src/ontology/templates/specimens.tsv index 25fd252e..1453e2c7 100644 --- a/src/ontology/templates/specimens.tsv +++ b/src/ontology/templates/specimens.tsv @@ -16,8 +16,8 @@ OBI:0000899 organellar RNA extract organellar RNA extract metadata complete A R OBI:0000902 post mortem specimen post mortem specimen metadata complete a specimen that was taken from a dead organism MO_416 postmortem the spleen taken from a dead mouse Bjoern Peters equivalent specimen with pre- or post-mortem status ('organism' and ('has quality' some 'dead')) OBI:0000908 labeled DNA extract labeled DNA extract metadata complete a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. Group: OBI group Group: OBI group Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call equivalent labeled nucleic acid extract ('addition of molecular label' and ('has_specified_input' some 'DNA extract')) 'has grain' some 'deoxyribonucleic acid' OBI:0000909 cloacal specimen cell specimen metadata complete A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium. WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf type of sample used in the PCIRN influenza network PERSON: Melanie Courtot equivalent specimen from organism collecting specimen from organism cloaca -OBI:0000914 nasopharyngeal aspirate specimen nasopharyngeal aspirate specimen metadata complete A specimen which derives from nasopharyngeal mucosa after aspiration. WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf type of sample used in the PCIRN influenza network PERSON: Melanie Courtot subclass specimen from organism collecting specimen from organism nasopharynx -OBI:0000917 nasal swab specimen nasal swab specimen metadata complete A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination. WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf type of sample used in the PCIRN influenza network PERSON: Melanie Courtot equivalent specimen from organism collecting specimen with swab nasal cavity mucosa +OBI:0000914 nasopharyngeal aspirate specimen nasopharyngeal aspirate specimen metadata complete A specimen which derives from nasopharyngeal mucosa after aspiration. WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf type of sample used in the PCIRN influenza network PERSON: Melanie Courtot subclass nasopharynx specimen collecting specimen from organism nasopharynx +OBI:0000917 nasal swab specimen nasal swab specimen metadata complete A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination. WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf type of sample used in the PCIRN influenza network PERSON: Melanie Courtot equivalent upper respiratory tract specimen collecting specimen with swab nasal cavity mucosa OBI:0000921 labeled RNA extract labeled RNA extract metadata complete a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments. Group: OBI group Group: OBI group Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call equivalent labeled nucleic acid extract ('addition of molecular label' and ('has_specified_input' some 'RNA extract')) 'has grain' some 'ribonucleic acid' OBI:0000922 frozen specimen frozen specimen metadata incomplete A specimen that has been frozen in order to store it. MO_610 frozen_sample Frozen blood plasma Person:Alan Ruttenberg equivalent specimen ('freezing storage' and ('has_specified_input' some ('has role' some 'specimen role'))) OBI:0000924 labeled specimen labeled specimen metadata incomplete A specimen that has been modified in order to be able to detect it in future experiments OBI group added during call 3/1/2010 equivalent specimen addition of molecular label 'has part' some 'molecular label' @@ -70,7 +70,7 @@ OBI:0002530 adipose tissue specimen ready for release A specimen that is deriv OBI:0002531 cortex of kidney specimen ready for release kidney cortex specimen A specimen that is derived from cortex of kidney. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'cortex of kidney')) UBERON_0001225 OBI:0002532 esophagus mucosa specimen ready for release A specimen that is derived from esophagus mucosa. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'esophagus mucosa')) UBERON_0002469 OBI:0002533 colon specimen ready for release A specimen that is derived from colon. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some colon)) UBERON_0001155 -OBI:0002534 lung specimen ready for release A specimen that is derived from lung. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some lung)) UBERON_0002048 +OBI:0002534 lung specimen ready for release A specimen that is derived from lung. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent lower respiratory tract specimen collecting specimen from organism (tissue and ('part of' some lung)) UBERON_0002048 OBI:0002535 esophagus muscularis mucosa specimen ready for release esophagus muscularis specimen A specimen that is derived from esophagus muscularis mucosa. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'esophagus muscularis mucosa')) UBERON_0004648 OBI:0002536 cerebral cortex specimen ready for release brain cortex specimen A specimen that is derived from cerebral cortex. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'cerebral cortex')) UBERON_0000956 OBI:0002537 thyroid gland specimen ready for release A specimen that is derived from thyroid gland. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'thyroid gland')) UBERON_0002046 @@ -96,9 +96,9 @@ OBI:0002599 swab specimen swab specimen ready for release A specimen that is st OBI:0002603 areolar swab specimen ready for release A specimen that is collected with a swab from the surface of an areola of a breast. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab areola UBERON_0002032 OBI:0002604 breast swab specimen ready for release A specimen that is collected with a swab from the surface of a breast. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab breast UBERON_0000310 OBI:0002605 cheek swab specimen ready for release A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab cheek UBERON_0001567 -OBI:0002606 nasopharyngeal swab specimen ready for release A specimen that is collected with a swab from the surface of a nasopharynx. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab nasopharynx UBERON_0001728 +OBI:0002606 nasopharyngeal swab specimen ready for release A specimen that is collected with a swab from the surface of a nasopharynx. Chris Stoeckert, OBIB Chris Stoeckert equivalent nasopharynx specimen collecting specimen with swab nasopharynx UBERON_0001728 OBI:0002607 oral swab specimen ready for release A specimen that is collected with a swab from the inside surface of a mouth. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab mouth UBERON_0000165 -OBI:0002608 oropharyngeal swab specimen ready for release A specimen that is collected with a swab from the surface of a oropharynx. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab oropharynx UBERON_0001729 +OBI:0002608 oropharyngeal swab specimen ready for release A specimen that is collected with a swab from the surface of a oropharynx. Chris Stoeckert, OBIB Chris Stoeckert equivalent upper respiratory tract specimen collecting specimen with swab oropharynx UBERON_0001729 OBI:0002609 rectal swab specimen ready for release A specimen that is collected with a swab from the surface of a rectum. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab rectum UBERON_0001052 OBI:0002610 tongue swab specimen ready for release A specimen that is collected with a swab from the surface of a tongue. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab tongue UBERON_0001723 OBI:0002611 vagina swab specimen ready for release A specimen that is collected with a swab from the surface of a vagina. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab vagina UBERON_0000996 @@ -109,14 +109,14 @@ OBI:0002648 individual organism specimen A specimen composed of an individual OBI:0002691 arthropod meal of blood specimen metadata complete blood meal A specimen of the blood ingested by an arthropod. VEuPathDB A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito. Chris Stoeckert|Jie Zheng The mosquito feeds on a human for example, ingests the blood of the human, this blood is then taken from the tummy of a mosquito and a PCR may be run on this specimen to identify that the mosquito definitely fed on a human. VEuPathDB https://github.com/obi-ontology/obi/issues/1117 subclass blood specimen collecting specimen from organism OBI:0002746 induced sputum specimen A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. PMC3297553 John Judkins subclass specimen from organism collecting specimen from organism sputum UBERON_0007311 OBI:0002774 platelet-poor plasma specimen A blood plasma specimen that is the output of some platelet-poor plasma preparation and is the portion of plasma that contains fewer than 10,000 platelets per microliter. PERSON: Matthew Diller subclass blood plasma specimen -OBI:0002778 tracheal aspirate specimen tracheal wash specimen A specimen that is collected with a suctioning tube from the trachea. PMID:25338241 Asiyah Yu Lin ORCID:0000-0003-2620-0345 subclass specimen from organism aspiration specimen collection trachea UBERON_0003126 -OBI:0002779 mid-turbinate nasal swab specimen A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity. https://seattlechildrenslab.testcatalog.org/catalogs/185/files/11633 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent specimen from organism collecting specimen with swab middle nasal concha UBERON_0005921 -OBI:0002780 nasal aspirate specimen nasal wash specimen|nasopharyngeal aspirate A specimen that is collected with a suctioning tube from the nasal cavity. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent specimen from organism aspiration specimen collection nasal cavity mucosa UBERON_0001826 -OBI:0002781 lower respiratory tract aspirate specimen lower respiratory tract wash specimen A specimen that is collected with a suctioning tube from the lower respiratory tract. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent specimen from organism aspiration specimen collection lower respiratory tract UBERON_0001558 -OBI:0002783 lower respiratory tract specimen A specimen that is derived from the lower respiratory tract. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent specimen from organism lower respiratory tract UBERON_0001558 -OBI:0002784 anterior nasal swab specimen A specimen that is derived from the anterior nasal wall Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent specimen from organism collecting specimen with swab anterior nasal wall UBERON_3000016 -OBI:0002971 endotracheal tube specimen A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea. https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 John Judkins ORCID:0000-0001-6595-0902 subclass specimen from organism collecting specimen from organism respiratory system fluid/secretion UBERON_0006538 -OBI:0002972 endotracheal aspirate specimen A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube. https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 John Judkins ORCID:0000-0001-6595-0902 subclass specimen from organism collecting specimen from organism respiratory system fluid/secretion UBERON_0006538 +OBI:0002778 tracheal aspirate specimen tracheal wash specimen A specimen that is collected with a suctioning tube from the trachea. PMID:25338241 Asiyah Yu Lin ORCID:0000-0003-2620-0345 subclass lower respiratory tract specimen aspiration specimen collection trachea UBERON_0003126 +OBI:0002779 mid-turbinate nasal swab specimen A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity. https://seattlechildrenslab.testcatalog.org/catalogs/185/files/11633 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent nasal swab specimen collecting specimen with swab middle nasal concha UBERON_0005921 +OBI:0002780 nasal aspirate specimen nasal wash specimen|nasopharyngeal aspirate A specimen that is collected with a suctioning tube from the nasal cavity. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent upper respiratory tract specimen aspiration specimen collection nasal cavity mucosa UBERON_0001826 +OBI:0002781 lower respiratory tract aspirate specimen lower respiratory tract wash specimen A specimen that is collected with a suctioning tube from the lower respiratory tract. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent lower respiratory tract specimen aspiration specimen collection lower respiratory tract UBERON_0001558 +OBI:0002783 lower respiratory tract specimen A specimen that is derived from the lower respiratory tract. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent respiratory system specimen lower respiratory tract UBERON_0001558 +OBI:0002784 anterior nasal swab specimen A specimen that is derived from the anterior nasal wall Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent nasal swab specimen collecting specimen with swab anterior nasal wall UBERON_3000016 +OBI:0002971 endotracheal tube specimen A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea. https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 John Judkins ORCID:0000-0001-6595-0902 subclass lower respiratory tract specimen collecting specimen from organism respiratory system fluid/secretion UBERON_0006538 +OBI:0002972 endotracheal aspirate specimen A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube. https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 John Judkins ORCID:0000-0001-6595-0902 subclass lower respiratory tract specimen collecting specimen from organism respiratory system fluid/secretion UBERON_0006538 OBI:0003054 blood specimen in vacutainer Vacutainer sample A blood specimen that is located in a vacutainer. VEuPathDB John Judkins subclass blood specimen collecting specimen from organism blood UBERON_0000178 OBI:0003055 blood specimen on filter paper Filter paper sample A blood specimen that is located on a filter paper. Penn Group Jie Zheng|Chris Stoeckert subclass blood specimen collecting specimen from organism blood UBERON_0000178 OBI:0003380 placental blood specimen A specimen that is derived from placental blood. VEuPathDB John Judkins equivalent blood specimen collecting specimen from organism placental blood UBERON_8470000 @@ -141,8 +141,8 @@ OBI:2000002 cervical mucus specimen A specimen that is derived from some cerv OBI:2000003 throat specimen A specimen that is derived from some throat Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some throat)) UBERON_0000341 OBI:2000004 eye specimen A specimen that is derived from some eye Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some eye)) UBERON_0000970 OBI:2000005 respiratory system specimen A specimen that is derived from some respiratory system Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'respiratory system')) UBERON_0001004 -OBI:2000006 upper respiratory tract specimen A specimen that is derived from some upper respiratory tract Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'upper respiratory tract')) UBERON_0001557 -OBI:2000007 nasopharynx specimen A specimen that is derived from some nasopharynx Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some nasopharynx)) UBERON_0001728 +OBI:2000006 upper respiratory tract specimen A specimen that is derived from some upper respiratory tract Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent respiratory system specimen collecting specimen from organism (tissue and ('part of' some 'upper respiratory tract')) UBERON_0001557 +OBI:2000007 nasopharynx specimen A specimen that is derived from some nasopharynx Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent upper respiratory tract specimen collecting specimen from organism (tissue and ('part of' some nasopharynx)) UBERON_0001728 OBI:2000008 semen specimen A specimen that is derived from some semen Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism semen UBERON_0001968 OBI:2000009 bodily fluid specimen A specimen that is derived from some bodily fluid Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism bodily fluid UBERON_0006314 OBI:2000010 chorionic villus specimen A specimen that is derived from some chorionic villus Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'chorionic villus')) UBERON_0007106 From f8403406c83d97231ca44b7933f60488b090af1f Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Wed, 27 Nov 2024 13:48:34 -0600 Subject: [PATCH 04/15] Oral & digestive tract specimen hierarchies --- src/ontology/modules/specimens.owl | 18 +++++++++--------- src/ontology/templates/specimens.tsv | 18 +++++++++--------- 2 files changed, 18 insertions(+), 18 deletions(-) diff --git a/src/ontology/modules/specimens.owl b/src/ontology/modules/specimens.owl index d8f1aa2a..21b384b4 100644 --- a/src/ontology/modules/specimens.owl +++ b/src/ontology/modules/specimens.owl @@ -2546,7 +2546,7 @@ - + @@ -2717,7 +2717,7 @@ - + @@ -2852,7 +2852,7 @@ - + @@ -3260,7 +3260,7 @@ - + @@ -3305,7 +3305,7 @@ - + @@ -3530,7 +3530,7 @@ - + @@ -3887,7 +3887,7 @@ - + @@ -4035,7 +4035,7 @@ - + @@ -4072,7 +4072,7 @@ - + diff --git a/src/ontology/templates/specimens.tsv b/src/ontology/templates/specimens.tsv index 1453e2c7..6da1e450 100644 --- a/src/ontology/templates/specimens.tsv +++ b/src/ontology/templates/specimens.tsv @@ -64,14 +64,14 @@ OBI:0002524 urinary bladder specimen ready for release A specimen that is deri OBI:0002525 tibial artery specimen ready for release A specimen that is derived from tibial artery. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'tibial artery')) UBERON_0007610 OBI:0002526 skin of body specimen ready for release skin specimen A specimen that is derived from skin. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'skin of body')) UBERON_0002097 OBI:0002527 pancreas specimen ready for release A specimen that is derived from pancreas. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some pancreas)) UBERON_0001264 -OBI:0002528 stomach specimen ready for release A specimen that is derived from stomach. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some stomach)) UBERON_0000945 +OBI:0002528 stomach specimen ready for release A specimen that is derived from stomach. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent digestive tract specimen collecting specimen from organism (tissue and ('part of' some stomach)) UBERON_0000945 OBI:0002529 pituitary gland specimen ready for release A specimen that is derived from pituitary gland. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'pituitary gland')) UBERON_0000007 OBI:0002530 adipose tissue specimen ready for release A specimen that is derived from adipose tissue. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism adipose tissue UBERON_0001013 OBI:0002531 cortex of kidney specimen ready for release kidney cortex specimen A specimen that is derived from cortex of kidney. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'cortex of kidney')) UBERON_0001225 -OBI:0002532 esophagus mucosa specimen ready for release A specimen that is derived from esophagus mucosa. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'esophagus mucosa')) UBERON_0002469 +OBI:0002532 esophagus mucosa specimen ready for release A specimen that is derived from esophagus mucosa. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent digestive tract specimen collecting specimen from organism (tissue and ('part of' some 'esophagus mucosa')) UBERON_0002469 OBI:0002533 colon specimen ready for release A specimen that is derived from colon. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some colon)) UBERON_0001155 OBI:0002534 lung specimen ready for release A specimen that is derived from lung. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent lower respiratory tract specimen collecting specimen from organism (tissue and ('part of' some lung)) UBERON_0002048 -OBI:0002535 esophagus muscularis mucosa specimen ready for release esophagus muscularis specimen A specimen that is derived from esophagus muscularis mucosa. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'esophagus muscularis mucosa')) UBERON_0004648 +OBI:0002535 esophagus muscularis mucosa specimen ready for release esophagus muscularis specimen A specimen that is derived from esophagus muscularis mucosa. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent digestive tract specimen collecting specimen from organism (tissue and ('part of' some 'esophagus muscularis mucosa')) UBERON_0004648 OBI:0002536 cerebral cortex specimen ready for release brain cortex specimen A specimen that is derived from cerebral cortex. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'cerebral cortex')) UBERON_0000956 OBI:0002537 thyroid gland specimen ready for release A specimen that is derived from thyroid gland. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'thyroid gland')) UBERON_0002046 OBI:0002538 cerebellum specimen ready for release brain cerebellum specimen A specimen that is derived from cerebellum. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some cerebellum)) UBERON_0002037 @@ -80,13 +80,13 @@ OBI:0002540 coronary artery specimen ready for release A specimen that is deri OBI:0002541 spleen specimen ready for release A specimen that is derived from spleen. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some spleen)) UBERON_0002106 OBI:0002542 aorta specimen ready for release A specimen that is derived from aorta. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some aorta)) UBERON_0000947 OBI:0002543 atrial appendage specimen ready for release A specimen that is derived from the atrium auricular region. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'atrium auricular region')) UBERON_0006618 -OBI:0002544 esophagogastric junction specimen ready for release A specimen that is derived from the esophagogastric junction. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'esophagogastric junction')) UBERON_0007650 -OBI:0002545 ileum specimen ready for release A specimen that is derived from ileum. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some ileum)) UBERON_0002116 +OBI:0002544 esophagogastric junction specimen ready for release A specimen that is derived from the esophagogastric junction. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent digestive tract specimen collecting specimen from organism (tissue and ('part of' some 'esophagogastric junction')) UBERON_0007650 +OBI:0002545 ileum specimen ready for release A specimen that is derived from ileum. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent digestive tract specimen collecting specimen from organism (tissue and ('part of' some ileum)) UBERON_0002116 OBI:0002546 liver specimen ready for release A specimen that is derived from liver. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some liver)) UBERON_0002107 OBI:0002547 minor salivary gland specimen ready for release A specimen that is derived from minor salivary gland. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'minor salivary gland')) UBERON_0001830 OBI:0002548 omentum specimen ready for release A specimen that is derived from omentum. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some omentum)) UBERON_0003688 OBI:0002549 ovary specimen ready for release A specimen that is derived from female gonad. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some ovary)) UBERON_0000992 -OBI:0002550 sigmoid colon specimen ready for release A specimen that is derived from sigmoid colon. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'sigmoid colon')) UBERON_0001159 +OBI:0002550 sigmoid colon specimen ready for release A specimen that is derived from sigmoid colon. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent digestive tract specimen collecting specimen from organism (tissue and ('part of' some 'sigmoid colon')) UBERON_0001159 OBI:0002551 suprapubic skin specimen ready for release A specimen that is derived from suprapubic skin. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'suprapubic skin')) UBERON_0036149 OBI:0002552 testis specimen ready for release A specimen that is derived from testis. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some testis)) UBERON_0000473 OBI:0002553 uterus specimen ready for release A specimen that is derived from uterus. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some uterus)) UBERON_0000995 @@ -95,12 +95,12 @@ OBI:0002573 polyA depleted RNA extract A RNA extract that is the output of an OBI:0002599 swab specimen swab specimen ready for release A specimen that is stored on a swab as the output of a collecting specimen with swab process. OBIB/OBI Chris Stoeckert OBIB https://github.com/obi-ontology/obi/issues/910 equivalent specimen collecting specimen with swab OBI:0002603 areolar swab specimen ready for release A specimen that is collected with a swab from the surface of an areola of a breast. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab areola UBERON_0002032 OBI:0002604 breast swab specimen ready for release A specimen that is collected with a swab from the surface of a breast. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab breast UBERON_0000310 -OBI:0002605 cheek swab specimen ready for release A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab cheek UBERON_0001567 +OBI:0002605 cheek swab specimen ready for release A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth. Chris Stoeckert, OBIB Chris Stoeckert equivalent oral swab specimen collecting specimen with swab cheek UBERON_0001567 OBI:0002606 nasopharyngeal swab specimen ready for release A specimen that is collected with a swab from the surface of a nasopharynx. Chris Stoeckert, OBIB Chris Stoeckert equivalent nasopharynx specimen collecting specimen with swab nasopharynx UBERON_0001728 OBI:0002607 oral swab specimen ready for release A specimen that is collected with a swab from the inside surface of a mouth. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab mouth UBERON_0000165 OBI:0002608 oropharyngeal swab specimen ready for release A specimen that is collected with a swab from the surface of a oropharynx. Chris Stoeckert, OBIB Chris Stoeckert equivalent upper respiratory tract specimen collecting specimen with swab oropharynx UBERON_0001729 -OBI:0002609 rectal swab specimen ready for release A specimen that is collected with a swab from the surface of a rectum. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab rectum UBERON_0001052 -OBI:0002610 tongue swab specimen ready for release A specimen that is collected with a swab from the surface of a tongue. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab tongue UBERON_0001723 +OBI:0002609 rectal swab specimen ready for release A specimen that is collected with a swab from the surface of a rectum. Chris Stoeckert, OBIB Chris Stoeckert equivalent digestive tract specimen collecting specimen with swab rectum UBERON_0001052 +OBI:0002610 tongue swab specimen ready for release A specimen that is collected with a swab from the surface of a tongue. Chris Stoeckert, OBIB Chris Stoeckert equivalent oral swab specimen collecting specimen with swab tongue UBERON_0001723 OBI:0002611 vagina swab specimen ready for release A specimen that is collected with a swab from the surface of a vagina. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab vagina UBERON_0000996 OBI:0002612 fecal swab specimen ready for release stool swab specimen A specimen that is collected with a swab from the surface of a feces. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab feces UBERON_0001988 OBI:0002613 environmental swab specimen ready for release A specimen that is collected with a swab from the surface of an environmenal material. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen collecting specimen with swab environmental material ENVO_00010483 From 704422717427cb6346739788a2460424a0a48810 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Wed, 27 Nov 2024 13:51:59 -0600 Subject: [PATCH 05/15] Brain specimen hierarchy --- src/ontology/modules/specimens.owl | 4 ++-- src/ontology/templates/specimens.tsv | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/ontology/modules/specimens.owl b/src/ontology/modules/specimens.owl index 21b384b4..49bf34bc 100644 --- a/src/ontology/modules/specimens.owl +++ b/src/ontology/modules/specimens.owl @@ -2898,7 +2898,7 @@ - + @@ -2989,7 +2989,7 @@ - + diff --git a/src/ontology/templates/specimens.tsv b/src/ontology/templates/specimens.tsv index 6da1e450..f7ee6c81 100644 --- a/src/ontology/templates/specimens.tsv +++ b/src/ontology/templates/specimens.tsv @@ -72,9 +72,9 @@ OBI:0002532 esophagus mucosa specimen ready for release A specimen that is der OBI:0002533 colon specimen ready for release A specimen that is derived from colon. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some colon)) UBERON_0001155 OBI:0002534 lung specimen ready for release A specimen that is derived from lung. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent lower respiratory tract specimen collecting specimen from organism (tissue and ('part of' some lung)) UBERON_0002048 OBI:0002535 esophagus muscularis mucosa specimen ready for release esophagus muscularis specimen A specimen that is derived from esophagus muscularis mucosa. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent digestive tract specimen collecting specimen from organism (tissue and ('part of' some 'esophagus muscularis mucosa')) UBERON_0004648 -OBI:0002536 cerebral cortex specimen ready for release brain cortex specimen A specimen that is derived from cerebral cortex. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'cerebral cortex')) UBERON_0000956 +OBI:0002536 cerebral cortex specimen ready for release brain cortex specimen A specimen that is derived from cerebral cortex. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent brain specimen collecting specimen from organism (tissue and ('part of' some 'cerebral cortex')) UBERON_0000956 OBI:0002537 thyroid gland specimen ready for release A specimen that is derived from thyroid gland. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'thyroid gland')) UBERON_0002046 -OBI:0002538 cerebellum specimen ready for release brain cerebellum specimen A specimen that is derived from cerebellum. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some cerebellum)) UBERON_0002037 +OBI:0002538 cerebellum specimen ready for release brain cerebellum specimen A specimen that is derived from cerebellum. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent brain specimen collecting specimen from organism (tissue and ('part of' some cerebellum)) UBERON_0002037 OBI:0002539 tibial nerve specimen ready for release A specimen that is derived from tibial nerve. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'tibial nerve')) UBERON_0001323 OBI:0002540 coronary artery specimen ready for release A specimen that is derived from coronary artery. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'coronary artery')) UBERON_0001621 OBI:0002541 spleen specimen ready for release A specimen that is derived from spleen. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some spleen)) UBERON_0002106 From e819225df06f50f189fced98b1b9446bee3e0fd7 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Wed, 27 Nov 2024 13:53:42 -0600 Subject: [PATCH 06/15] Breast specimen hierarchy --- src/ontology/modules/specimens.owl | 4 ++-- src/ontology/templates/specimens.tsv | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/ontology/modules/specimens.owl b/src/ontology/modules/specimens.owl index 49bf34bc..3f61fd73 100644 --- a/src/ontology/modules/specimens.owl +++ b/src/ontology/modules/specimens.owl @@ -3813,7 +3813,7 @@ - + @@ -3850,7 +3850,7 @@ - + diff --git a/src/ontology/templates/specimens.tsv b/src/ontology/templates/specimens.tsv index f7ee6c81..73cf2f29 100644 --- a/src/ontology/templates/specimens.tsv +++ b/src/ontology/templates/specimens.tsv @@ -93,8 +93,8 @@ OBI:0002553 uterus specimen ready for release A specimen that is derived from OBI:0002554 vagina specimen ready for release A specimen that is derived from vagina. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some vagina)) UBERON_0000996 OBI:0002573 polyA depleted RNA extract A RNA extract that is the output of an extraction process in which RNA molecules lacking poly A tails at thier 3' ends are purified. UPenn Group PERSON: Chris Stoeckert|PERSON: Jie Zheng|Mark A. Miller, based on http://purl.obolibrary.org/obo/OBI_0000869 subclass RNA extract RNA extraction with polyA depletion OBI:0002599 swab specimen swab specimen ready for release A specimen that is stored on a swab as the output of a collecting specimen with swab process. OBIB/OBI Chris Stoeckert OBIB https://github.com/obi-ontology/obi/issues/910 equivalent specimen collecting specimen with swab -OBI:0002603 areolar swab specimen ready for release A specimen that is collected with a swab from the surface of an areola of a breast. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab areola UBERON_0002032 -OBI:0002604 breast swab specimen ready for release A specimen that is collected with a swab from the surface of a breast. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab breast UBERON_0000310 +OBI:0002603 areolar swab specimen ready for release A specimen that is collected with a swab from the surface of an areola of a breast. Chris Stoeckert, OBIB Chris Stoeckert equivalent breast swab specimen collecting specimen with swab areola UBERON_0002032 +OBI:0002604 breast swab specimen ready for release A specimen that is collected with a swab from the surface of a breast. Chris Stoeckert, OBIB Chris Stoeckert equivalent breast specimen collecting specimen with swab breast UBERON_0000310 OBI:0002605 cheek swab specimen ready for release A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth. Chris Stoeckert, OBIB Chris Stoeckert equivalent oral swab specimen collecting specimen with swab cheek UBERON_0001567 OBI:0002606 nasopharyngeal swab specimen ready for release A specimen that is collected with a swab from the surface of a nasopharynx. Chris Stoeckert, OBIB Chris Stoeckert equivalent nasopharynx specimen collecting specimen with swab nasopharynx UBERON_0001728 OBI:0002607 oral swab specimen ready for release A specimen that is collected with a swab from the inside surface of a mouth. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab mouth UBERON_0000165 From ea01a66641a2eab5a47d9ac718ac3dd9fd859d46 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Wed, 27 Nov 2024 13:55:40 -0600 Subject: [PATCH 07/15] Feces specimen hierarchy --- src/ontology/modules/specimens.owl | 4 ++-- src/ontology/templates/specimens.tsv | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/ontology/modules/specimens.owl b/src/ontology/modules/specimens.owl index 3f61fd73..2a4780a1 100644 --- a/src/ontology/modules/specimens.owl +++ b/src/ontology/modules/specimens.owl @@ -4146,7 +4146,7 @@ - + @@ -5785,7 +5785,7 @@ - + diff --git a/src/ontology/templates/specimens.tsv b/src/ontology/templates/specimens.tsv index 73cf2f29..d286accb 100644 --- a/src/ontology/templates/specimens.tsv +++ b/src/ontology/templates/specimens.tsv @@ -102,7 +102,7 @@ OBI:0002608 oropharyngeal swab specimen ready for release A specimen that is c OBI:0002609 rectal swab specimen ready for release A specimen that is collected with a swab from the surface of a rectum. Chris Stoeckert, OBIB Chris Stoeckert equivalent digestive tract specimen collecting specimen with swab rectum UBERON_0001052 OBI:0002610 tongue swab specimen ready for release A specimen that is collected with a swab from the surface of a tongue. Chris Stoeckert, OBIB Chris Stoeckert equivalent oral swab specimen collecting specimen with swab tongue UBERON_0001723 OBI:0002611 vagina swab specimen ready for release A specimen that is collected with a swab from the surface of a vagina. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab vagina UBERON_0000996 -OBI:0002612 fecal swab specimen ready for release stool swab specimen A specimen that is collected with a swab from the surface of a feces. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab feces UBERON_0001988 +OBI:0002612 fecal swab specimen ready for release stool swab specimen A specimen that is collected with a swab from the surface of a feces. Chris Stoeckert, OBIB Chris Stoeckert equivalent feces specimen collecting specimen with swab feces UBERON_0001988 OBI:0002613 environmental swab specimen ready for release A specimen that is collected with a swab from the surface of an environmenal material. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen collecting specimen with swab environmental material ENVO_00010483 OBI:0002627 ribosomal RNA-depleted RNA extract ribosomal RNA-depleted RNA extract pending final vetting An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species). https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1 Looking at the reads for each ribosomal RNA-depleted RNA extract, the vast majority align to protein coding genes based on the ENSEMBL annotation. Dan Berrios subclass RNA extract OBI:0002648 individual organism specimen A specimen composed of an individual organism to be studied in an investigation. EFO_0000542 individual Person: Jie Zheng https://github.com/obi-ontology/obi/issues/1092 equivalent specimen 'has component' exactly 1 'organism' @@ -146,7 +146,7 @@ OBI:2000007 nasopharynx specimen A specimen that is derived from some nasopha OBI:2000008 semen specimen A specimen that is derived from some semen Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism semen UBERON_0001968 OBI:2000009 bodily fluid specimen A specimen that is derived from some bodily fluid Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism bodily fluid UBERON_0006314 OBI:2000010 chorionic villus specimen A specimen that is derived from some chorionic villus Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'chorionic villus')) UBERON_0007106 -OBI:2000011 meconium specimen A specimen that is derived from some meconium Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism meconium UBERON_0007109 +OBI:2000011 meconium specimen A specimen that is derived from some meconium Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent feces specimen collecting specimen from organism meconium UBERON_0007109 OBI:2000012 umbilical cord blood specimen A specimen that is derived from some umbilical cord blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent blood specimen collecting specimen from organism umbilical cord blood UBERON_0012168 OBI:2000013 arterial blood specimen A specimen that is derived from some arterial blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent blood specimen collecting specimen from organism arterial blood UBERON_0013755 OBI:2000014 venous blood specimen A specimen that is derived from some venous blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent blood specimen collecting specimen from organism venous blood UBERON_0013756 From 5429c610549c90c44ddf93fd957827a2385ae6c2 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Wed, 27 Nov 2024 13:56:44 -0600 Subject: [PATCH 08/15] Eye specimen hierarchy --- src/ontology/modules/specimens.owl | 2 +- src/ontology/templates/specimens.tsv | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontology/modules/specimens.owl b/src/ontology/modules/specimens.owl index 2a4780a1..4552aee1 100644 --- a/src/ontology/modules/specimens.owl +++ b/src/ontology/modules/specimens.owl @@ -1827,7 +1827,7 @@ - + diff --git a/src/ontology/templates/specimens.tsv b/src/ontology/templates/specimens.tsv index d286accb..b08124e4 100644 --- a/src/ontology/templates/specimens.tsv +++ b/src/ontology/templates/specimens.tsv @@ -47,7 +47,7 @@ OBI:0002507 saliva specimen ready for release A specimen that is derived from OBI:0002508 sputum specimen ready for release A specimen that is derived from sputum. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism sputum UBERON_0007311 OBI:0002509 sweat specimen ready for release A specimen that is derived from sweat. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism sweat UBERON_0001089 OBI:0002510 synovial fluid specimen ready for release A specimen that is derived from synovial fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism synovial fluid UBERON_0001090 -OBI:0002511 vitreous humor specimen ready for release vitreous fluid specimen A specimen that is derived from vireous humor. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'vitreous humor')) UBERON_0001797 +OBI:0002511 vitreous humor specimen ready for release vitreous fluid specimen A specimen that is derived from vireous humor. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent eye specimen collecting specimen from organism (tissue and ('part of' some 'vitreous humor')) UBERON_0001797 OBI:0002512 bone marrow specimen ready for release A specimen that is derived from bone marrow. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism bone marrow biopsy bone marrow UBERON_0002371 OBI:0002513 placenta specimen ready for release A specimen that is derived from placenta. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some placenta)) UBERON_0001987 OBI:0002514 peritoneal fluid specimen ready for release A specimen that is derived from peritoneal fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism peritoneal fluid UBERON_0001268 From 19a0722633a7849599a3637f575dd6d774ee9b70 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Wed, 27 Nov 2024 14:01:36 -0600 Subject: [PATCH 09/15] Vagina, uterus, placenta specimen hierarchies --- src/ontology/modules/specimens.owl | 6 +++--- src/ontology/templates/specimens.tsv | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/ontology/modules/specimens.owl b/src/ontology/modules/specimens.owl index 4552aee1..d66d96d7 100644 --- a/src/ontology/modules/specimens.owl +++ b/src/ontology/modules/specimens.owl @@ -4109,7 +4109,7 @@ - + @@ -5309,7 +5309,7 @@ - + @@ -5739,7 +5739,7 @@ - + diff --git a/src/ontology/templates/specimens.tsv b/src/ontology/templates/specimens.tsv index b08124e4..1459d465 100644 --- a/src/ontology/templates/specimens.tsv +++ b/src/ontology/templates/specimens.tsv @@ -101,7 +101,7 @@ OBI:0002607 oral swab specimen ready for release A specimen that is collected OBI:0002608 oropharyngeal swab specimen ready for release A specimen that is collected with a swab from the surface of a oropharynx. Chris Stoeckert, OBIB Chris Stoeckert equivalent upper respiratory tract specimen collecting specimen with swab oropharynx UBERON_0001729 OBI:0002609 rectal swab specimen ready for release A specimen that is collected with a swab from the surface of a rectum. Chris Stoeckert, OBIB Chris Stoeckert equivalent digestive tract specimen collecting specimen with swab rectum UBERON_0001052 OBI:0002610 tongue swab specimen ready for release A specimen that is collected with a swab from the surface of a tongue. Chris Stoeckert, OBIB Chris Stoeckert equivalent oral swab specimen collecting specimen with swab tongue UBERON_0001723 -OBI:0002611 vagina swab specimen ready for release A specimen that is collected with a swab from the surface of a vagina. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen from organism collecting specimen with swab vagina UBERON_0000996 +OBI:0002611 vagina swab specimen ready for release A specimen that is collected with a swab from the surface of a vagina. Chris Stoeckert, OBIB Chris Stoeckert equivalent vagina specimen collecting specimen with swab vagina UBERON_0000996 OBI:0002612 fecal swab specimen ready for release stool swab specimen A specimen that is collected with a swab from the surface of a feces. Chris Stoeckert, OBIB Chris Stoeckert equivalent feces specimen collecting specimen with swab feces UBERON_0001988 OBI:0002613 environmental swab specimen ready for release A specimen that is collected with a swab from the surface of an environmenal material. Chris Stoeckert, OBIB Chris Stoeckert equivalent specimen collecting specimen with swab environmental material ENVO_00010483 OBI:0002627 ribosomal RNA-depleted RNA extract ribosomal RNA-depleted RNA extract pending final vetting An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species). https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1 Looking at the reads for each ribosomal RNA-depleted RNA extract, the vast majority align to protein coding genes based on the ENSEMBL annotation. Dan Berrios subclass RNA extract @@ -135,7 +135,7 @@ OBI:1000049 whole mount tissue whole mount tissue metadata complete whole mount OBI:1110041 lymph node cell specimen lymph node cell specimen metadata incomplete A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types. IEDB IEDB equivalent cell specimen ('organ harvesting' and ('has_specified_input' some 'lymph node')) OBI:1110116 splenocyte specimen splenocyte specimen metadata complete A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types. IEDB IEDB equivalent cell specimen ('organ harvesting' and ('has_specified_input' some 'spleen')) OBI:1200000 FFPE specimen FFPE specimen formalin-fixed paraffin-embeded specimen A specimen that has been fixed in formalin and embedded in paraffin. https://www.biochain.com/general/what-is-ffpe-tissue/ Many of today’s researchers prefer to use Formalin-Fixed Paraffin-Embedded samples of tissues for their IHC, histological or in-situ genomic analyses. Professionally fixed and embedded FFPE samples and the biomolecules they contain are reasonably stable at ambient temperatures. -based on https://lab-ally.com/histopathology-resources/ffpe-samples/ MIABIS https://github.com/obi-ontology/obi/issues/1019 subclass paraffin specimen -OBI:2000000 uterine cervix specimen A specimen that is derived from some uterine cervix Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'uterine cervix')) UBERON_0000002 +OBI:2000000 uterine cervix specimen A specimen that is derived from some uterine cervix Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent uterus specimen collecting specimen from organism (tissue and ('part of' some 'uterine cervix')) UBERON_0000002 OBI:2000001 urethra specimen A specimen that is derived from some urethra Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some urethra)) UBERON_0000057 OBI:2000002 cervical mucus specimen A specimen that is derived from some cervical mucus Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism cervical mucus UBERON_0000316 OBI:2000003 throat specimen A specimen that is derived from some throat Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some throat)) UBERON_0000341 @@ -145,7 +145,7 @@ OBI:2000006 upper respiratory tract specimen A specimen that is derived from OBI:2000007 nasopharynx specimen A specimen that is derived from some nasopharynx Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent upper respiratory tract specimen collecting specimen from organism (tissue and ('part of' some nasopharynx)) UBERON_0001728 OBI:2000008 semen specimen A specimen that is derived from some semen Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism semen UBERON_0001968 OBI:2000009 bodily fluid specimen A specimen that is derived from some bodily fluid Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism bodily fluid UBERON_0006314 -OBI:2000010 chorionic villus specimen A specimen that is derived from some chorionic villus Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'chorionic villus')) UBERON_0007106 +OBI:2000010 chorionic villus specimen A specimen that is derived from some chorionic villus Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent placenta specimen collecting specimen from organism (tissue and ('part of' some 'chorionic villus')) UBERON_0007106 OBI:2000011 meconium specimen A specimen that is derived from some meconium Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent feces specimen collecting specimen from organism meconium UBERON_0007109 OBI:2000012 umbilical cord blood specimen A specimen that is derived from some umbilical cord blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent blood specimen collecting specimen from organism umbilical cord blood UBERON_0012168 OBI:2000013 arterial blood specimen A specimen that is derived from some arterial blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent blood specimen collecting specimen from organism arterial blood UBERON_0013755 From 711716524c9f265e18470d9cc68f08a9e69a5bcb Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Wed, 27 Nov 2024 14:03:58 -0600 Subject: [PATCH 10/15] Skin pecimen hierarchy --- src/ontology/modules/specimens.owl | 2 +- src/ontology/templates/specimens.tsv | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontology/modules/specimens.owl b/src/ontology/modules/specimens.owl index d66d96d7..8cb15398 100644 --- a/src/ontology/modules/specimens.owl +++ b/src/ontology/modules/specimens.owl @@ -3575,7 +3575,7 @@ - + diff --git a/src/ontology/templates/specimens.tsv b/src/ontology/templates/specimens.tsv index 1459d465..c194a0c5 100644 --- a/src/ontology/templates/specimens.tsv +++ b/src/ontology/templates/specimens.tsv @@ -87,7 +87,7 @@ OBI:0002547 minor salivary gland specimen ready for release A specimen that is OBI:0002548 omentum specimen ready for release A specimen that is derived from omentum. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some omentum)) UBERON_0003688 OBI:0002549 ovary specimen ready for release A specimen that is derived from female gonad. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some ovary)) UBERON_0000992 OBI:0002550 sigmoid colon specimen ready for release A specimen that is derived from sigmoid colon. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent digestive tract specimen collecting specimen from organism (tissue and ('part of' some 'sigmoid colon')) UBERON_0001159 -OBI:0002551 suprapubic skin specimen ready for release A specimen that is derived from suprapubic skin. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'suprapubic skin')) UBERON_0036149 +OBI:0002551 suprapubic skin specimen ready for release A specimen that is derived from suprapubic skin. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent skin of body specimen collecting specimen from organism (tissue and ('part of' some 'suprapubic skin')) UBERON_0036149 OBI:0002552 testis specimen ready for release A specimen that is derived from testis. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some testis)) UBERON_0000473 OBI:0002553 uterus specimen ready for release A specimen that is derived from uterus. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some uterus)) UBERON_0000995 OBI:0002554 vagina specimen ready for release A specimen that is derived from vagina. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some vagina)) UBERON_0000996 From 507696a8fefb7ae143f83f6fd4845fe56f605a29 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Wed, 27 Nov 2024 14:04:53 -0600 Subject: [PATCH 11/15] Add colon specimen to digestive tract specimen hierarchy --- src/ontology/modules/specimens.owl | 2 +- src/ontology/templates/specimens.tsv | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontology/modules/specimens.owl b/src/ontology/modules/specimens.owl index 8cb15398..b3b8c1a4 100644 --- a/src/ontology/modules/specimens.owl +++ b/src/ontology/modules/specimens.owl @@ -2762,7 +2762,7 @@ - + diff --git a/src/ontology/templates/specimens.tsv b/src/ontology/templates/specimens.tsv index c194a0c5..2c206ff9 100644 --- a/src/ontology/templates/specimens.tsv +++ b/src/ontology/templates/specimens.tsv @@ -69,7 +69,7 @@ OBI:0002529 pituitary gland specimen ready for release A specimen that is deri OBI:0002530 adipose tissue specimen ready for release A specimen that is derived from adipose tissue. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism adipose tissue UBERON_0001013 OBI:0002531 cortex of kidney specimen ready for release kidney cortex specimen A specimen that is derived from cortex of kidney. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'cortex of kidney')) UBERON_0001225 OBI:0002532 esophagus mucosa specimen ready for release A specimen that is derived from esophagus mucosa. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent digestive tract specimen collecting specimen from organism (tissue and ('part of' some 'esophagus mucosa')) UBERON_0002469 -OBI:0002533 colon specimen ready for release A specimen that is derived from colon. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some colon)) UBERON_0001155 +OBI:0002533 colon specimen ready for release A specimen that is derived from colon. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent digestive tract specimen collecting specimen from organism (tissue and ('part of' some colon)) UBERON_0001155 OBI:0002534 lung specimen ready for release A specimen that is derived from lung. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent lower respiratory tract specimen collecting specimen from organism (tissue and ('part of' some lung)) UBERON_0002048 OBI:0002535 esophagus muscularis mucosa specimen ready for release esophagus muscularis specimen A specimen that is derived from esophagus muscularis mucosa. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent digestive tract specimen collecting specimen from organism (tissue and ('part of' some 'esophagus muscularis mucosa')) UBERON_0004648 OBI:0002536 cerebral cortex specimen ready for release brain cortex specimen A specimen that is derived from cerebral cortex. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent brain specimen collecting specimen from organism (tissue and ('part of' some 'cerebral cortex')) UBERON_0000956 From 48aa576295bab2af628c3c12e8309119d5f9a3ae Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Wed, 27 Nov 2024 14:14:49 -0600 Subject: [PATCH 12/15] Bodily fluid specimen hierarchy --- src/ontology/modules/specimens.owl | 82 ++++++++++++++-------------- src/ontology/templates/specimens.tsv | 34 ++++++------ 2 files changed, 59 insertions(+), 57 deletions(-) diff --git a/src/ontology/modules/specimens.owl b/src/ontology/modules/specimens.owl index b3b8c1a4..2538379a 100644 --- a/src/ontology/modules/specimens.owl +++ b/src/ontology/modules/specimens.owl @@ -248,7 +248,7 @@ - + @@ -291,7 +291,7 @@ - + @@ -1440,7 +1440,7 @@ - + @@ -1475,7 +1475,7 @@ - + @@ -1510,7 +1510,7 @@ - + @@ -1581,7 +1581,7 @@ - + @@ -1617,7 +1617,7 @@ - + @@ -1652,7 +1652,7 @@ - + @@ -1687,7 +1687,7 @@ - + @@ -1722,7 +1722,7 @@ - + @@ -1757,7 +1757,7 @@ - + @@ -1792,7 +1792,7 @@ - + @@ -1953,7 +1953,7 @@ - + @@ -1988,7 +1988,7 @@ - + @@ -4294,7 +4294,7 @@ - + @@ -4756,37 +4756,39 @@ - - + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - + - - - - - - - + A specimen that is derived from a portion of lymph collected from an organism. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB @@ -5667,7 +5669,7 @@ - + diff --git a/src/ontology/templates/specimens.tsv b/src/ontology/templates/specimens.tsv index 2c206ff9..5ed3dc5b 100644 --- a/src/ontology/templates/specimens.tsv +++ b/src/ontology/templates/specimens.tsv @@ -1,7 +1,7 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class specimen collection process gross anatomical part collection process input associated axioms URI ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C is_specified_output_of some % C (is_specified_output_of some 'specimen collection process') and ('derives from' some %) C is_specified_output_of some ('specimen collection process' and has_specified_input some %) C % SPLIT=| -OBI:0000651 urine specimen urine specimen metadata complete a portion of urine collected from an organism This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active|are we happy calling collection of urine a material separation?|4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant. equivalent specimen from organism collecting specimen from organism urine -OBI:0000655 blood specimen blood specimen ready for release a material entity derived from a portion of blood collected from an organism Bjoern Peters blood drawn from a human for glucose assay Bjoern Peters equivalent specimen from organism collecting specimen from organism blood +OBI:0000651 urine specimen urine specimen metadata complete a portion of urine collected from an organism This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active|are we happy calling collection of urine a material separation?|4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant. equivalent bodily fluid specimen collecting specimen from organism urine +OBI:0000655 blood specimen blood specimen ready for release a material entity derived from a portion of blood collected from an organism Bjoern Peters blood drawn from a human for glucose assay Bjoern Peters equivalent bodily fluid specimen collecting specimen from organism blood OBI:0000671 sample from organism sample from organism example to be eventually removed a material obtained from an organism in order to be a representative of the whole we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.|5/29: This is a helper class for now equivalent specimen from organism 'has role' some 'material sample role' OBI:0000680 whole organism preparation whole organism preparation metadata incomplete A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained putting a mouse in the blender. Not: putting a mouse on a scale does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged. subclass specimen 'derives from' some 'organism' OBI:0000747 material sample material sample metadata incomplete sample|sample population A material entity that has the material sample role blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. OBI: workshop https://github.com/obi-ontology/obi/issues/1013 equivalent specimen 'has role' some 'material sample role' @@ -36,22 +36,22 @@ OBI:0001506 specimen with pre- or post-mortem status specimen with pre- or post- OBI:0002125 H&E-stained fixed tissue slide specimen H&E-stained fixed tissue slide specimen pending final vetting A fixed tissue slide specimen that is the output of H&E slide staining. OBIB, OBI Chris Stoeckert, Ned Haubein equivalent fixed tissue slide specimen H&E slide staining OBI:0002126 IHC-stained fixed tissue slide specimen IHC-stained fixed tissue slide specimen pending final vetting A fixed tissue slide specimen that is the output of immunohistochemistry slide staining. OBIB, OBI Chris Stoeckert, Ned Haubein equivalent fixed tissue slide specimen IHC slide staining OBI:0002127 single cell specimen metadata complete A cell specimen that contains only one cell. PERSON: Jie Zheng, Alexander Diehl PERSON: Jie Zheng, Alexander Diehl Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/ subclass cell specimen -OBI:0002500 amniotic fluid specimen ready for release A specimen that is derived from amniotic fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism amniotic fluid UBERON_0000173 -OBI:0002501 bile specimen ready for release A specimen that is derived from bile. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism bile UBERON_0001970 -OBI:0002502 cerebrospinal fluid specimen ready for release A specimen that is derived from cerbrospinal fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism cerebrospinal fluid UBERON_0001359 +OBI:0002500 amniotic fluid specimen ready for release A specimen that is derived from amniotic fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent bodily fluid specimen collecting specimen from organism amniotic fluid UBERON_0000173 +OBI:0002501 bile specimen ready for release A specimen that is derived from bile. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent digestive system fluid or secretion specimen collecting specimen from organism bile UBERON_0001970 +OBI:0002502 cerebrospinal fluid specimen ready for release A specimen that is derived from cerbrospinal fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent bodily fluid specimen collecting specimen from organism cerebrospinal fluid UBERON_0001359 OBI:0002503 feces specimen ready for release stool specimen A specimen that is derived from feces. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism feces UBERON_0001988 -OBI:0002504 digestive system fluid or secretion specimen ready for release gastric fluid specimen A specimen that is derived from digestive system fluid or secretion. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism digestive system secreted substance UBERON_0006911 -OBI:0002505 milk specimen ready for release A specimen that is derived from milk. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism milk UBERON_0001913 -OBI:0002506 pericardial fluid specimen ready for release A specimen that is derived from pericardial fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism pericardial fluid UBERON_0002409 -OBI:0002507 saliva specimen ready for release A specimen that is derived from saliva. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism saliva UBERON_0001836 -OBI:0002508 sputum specimen ready for release A specimen that is derived from sputum. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism sputum UBERON_0007311 -OBI:0002509 sweat specimen ready for release A specimen that is derived from sweat. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism sweat UBERON_0001089 -OBI:0002510 synovial fluid specimen ready for release A specimen that is derived from synovial fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism synovial fluid UBERON_0001090 +OBI:0002504 digestive system fluid or secretion specimen ready for release gastric fluid specimen A specimen that is derived from digestive system fluid or secretion. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent bodily fluid specimen collecting specimen from organism digestive system secreted substance UBERON_0006911 +OBI:0002505 milk specimen ready for release A specimen that is derived from milk. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent bodily fluid specimen collecting specimen from organism milk UBERON_0001913 +OBI:0002506 pericardial fluid specimen ready for release A specimen that is derived from pericardial fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent bodily fluid specimen collecting specimen from organism pericardial fluid UBERON_0002409 +OBI:0002507 saliva specimen ready for release A specimen that is derived from saliva. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent bodily fluid specimen collecting specimen from organism saliva UBERON_0001836 +OBI:0002508 sputum specimen ready for release A specimen that is derived from sputum. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent bodily fluid specimen collecting specimen from organism sputum UBERON_0007311 +OBI:0002509 sweat specimen ready for release A specimen that is derived from sweat. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent bodily fluid specimen collecting specimen from organism sweat UBERON_0001089 +OBI:0002510 synovial fluid specimen ready for release A specimen that is derived from synovial fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent bodily fluid specimen collecting specimen from organism synovial fluid UBERON_0001090 OBI:0002511 vitreous humor specimen ready for release vitreous fluid specimen A specimen that is derived from vireous humor. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent eye specimen collecting specimen from organism (tissue and ('part of' some 'vitreous humor')) UBERON_0001797 OBI:0002512 bone marrow specimen ready for release A specimen that is derived from bone marrow. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism bone marrow biopsy bone marrow UBERON_0002371 OBI:0002513 placenta specimen ready for release A specimen that is derived from placenta. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some placenta)) UBERON_0001987 -OBI:0002514 peritoneal fluid specimen ready for release A specimen that is derived from peritoneal fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism peritoneal fluid UBERON_0001268 -OBI:0002515 pleural fluid specimen ready for release A specimen that is derived from pleural fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent specimen from organism collecting specimen from organism pleural fluid UBERON_0001087 +OBI:0002514 peritoneal fluid specimen ready for release A specimen that is derived from peritoneal fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent bodily fluid specimen collecting specimen from organism peritoneal fluid UBERON_0001268 +OBI:0002515 pleural fluid specimen ready for release A specimen that is derived from pleural fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent bodily fluid specimen collecting specimen from organism pleural fluid UBERON_0001087 OBI:0002516 brain specimen ready for release A specimen that is derived from brain. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some brain)) UBERON_0000955 OBI:0002517 hair specimen ready for release A specimen that is derived from hair. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism strand of hair UBERON_0001037 OBI:0002518 prostate gland specimen ready for release A specimen that is derived from prostate gland. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'prostate gland')) UBERON_0002367 @@ -107,7 +107,7 @@ OBI:0002613 environmental swab specimen ready for release A specimen that is c OBI:0002627 ribosomal RNA-depleted RNA extract ribosomal RNA-depleted RNA extract pending final vetting An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species). https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1 Looking at the reads for each ribosomal RNA-depleted RNA extract, the vast majority align to protein coding genes based on the ENSEMBL annotation. Dan Berrios subclass RNA extract OBI:0002648 individual organism specimen A specimen composed of an individual organism to be studied in an investigation. EFO_0000542 individual Person: Jie Zheng https://github.com/obi-ontology/obi/issues/1092 equivalent specimen 'has component' exactly 1 'organism' OBI:0002691 arthropod meal of blood specimen metadata complete blood meal A specimen of the blood ingested by an arthropod. VEuPathDB A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito. Chris Stoeckert|Jie Zheng The mosquito feeds on a human for example, ingests the blood of the human, this blood is then taken from the tummy of a mosquito and a PCR may be run on this specimen to identify that the mosquito definitely fed on a human. VEuPathDB https://github.com/obi-ontology/obi/issues/1117 subclass blood specimen collecting specimen from organism -OBI:0002746 induced sputum specimen A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. PMC3297553 John Judkins subclass specimen from organism collecting specimen from organism sputum UBERON_0007311 +OBI:0002746 induced sputum specimen A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. PMC3297553 John Judkins subclass sputum specimen collecting specimen from organism sputum UBERON_0007311 OBI:0002774 platelet-poor plasma specimen A blood plasma specimen that is the output of some platelet-poor plasma preparation and is the portion of plasma that contains fewer than 10,000 platelets per microliter. PERSON: Matthew Diller subclass blood plasma specimen OBI:0002778 tracheal aspirate specimen tracheal wash specimen A specimen that is collected with a suctioning tube from the trachea. PMID:25338241 Asiyah Yu Lin ORCID:0000-0003-2620-0345 subclass lower respiratory tract specimen aspiration specimen collection trachea UBERON_0003126 OBI:0002779 mid-turbinate nasal swab specimen A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity. https://seattlechildrenslab.testcatalog.org/catalogs/185/files/11633 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent nasal swab specimen collecting specimen with swab middle nasal concha UBERON_0005921 @@ -121,7 +121,7 @@ OBI:0003054 blood specimen in vacutainer Vacutainer sample A blood specimen th OBI:0003055 blood specimen on filter paper Filter paper sample A blood specimen that is located on a filter paper. Penn Group Jie Zheng|Chris Stoeckert subclass blood specimen collecting specimen from organism blood UBERON_0000178 OBI:0003380 placental blood specimen A specimen that is derived from placental blood. VEuPathDB John Judkins equivalent blood specimen collecting specimen from organism placental blood UBERON_8470000 OBI:0003415 peripheral blood mononuclear cell specimen PBMC specimen A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system. http://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell Jie Zheng|Chris Stoeckert subclass blood specimen collecting specimen from organism peripheral blood mononuclear cell CL_2000001 -OBI:0003482 lymph specimen A specimen that is derived from a portion of lymph collected from an organism. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 specimen from organism collecting specimen from organism (tissue and ('part of' some lymph)) UBERON_0002391 +OBI:0003482 lymph specimen A specimen that is derived from a portion of lymph collected from an organism. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 equivalent bodily fluid specimen collecting specimen from organism (tissue and ('part of' some lymph)) UBERON_0002391 OBI:0003483 digestive tract specimen A specimen that is derived from part of a digestive tract. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 specimen from organism collecting specimen from organism (tissue and ('part of' some 'digestive tract')) UBERON_0001555 OBI:0003595 nasal lavage fluid A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space. Sebastian Duesing|Randi Vita equivalent lavage fluid specimen lavage nasal cavity mucosa UBERON_0001826 OBI:0003652 albumin-free serum albumin-free serum A blood serum specimen that contains no albumin. Sebastian Duesing Philippe Rocca-Serra https://github.com/obi-ontology/obi/issues/493 equivalent blood serum specimen 'has part' only (not ('albumin')) @@ -143,7 +143,7 @@ OBI:2000004 eye specimen A specimen that is derived from some eye Mark A. Mil OBI:2000005 respiratory system specimen A specimen that is derived from some respiratory system Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'respiratory system')) UBERON_0001004 OBI:2000006 upper respiratory tract specimen A specimen that is derived from some upper respiratory tract Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent respiratory system specimen collecting specimen from organism (tissue and ('part of' some 'upper respiratory tract')) UBERON_0001557 OBI:2000007 nasopharynx specimen A specimen that is derived from some nasopharynx Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent upper respiratory tract specimen collecting specimen from organism (tissue and ('part of' some nasopharynx)) UBERON_0001728 -OBI:2000008 semen specimen A specimen that is derived from some semen Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism semen UBERON_0001968 +OBI:2000008 semen specimen A specimen that is derived from some semen Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent bodily fluid specimen collecting specimen from organism semen UBERON_0001968 OBI:2000009 bodily fluid specimen A specimen that is derived from some bodily fluid Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen from organism bodily fluid UBERON_0006314 OBI:2000010 chorionic villus specimen A specimen that is derived from some chorionic villus Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent placenta specimen collecting specimen from organism (tissue and ('part of' some 'chorionic villus')) UBERON_0007106 OBI:2000011 meconium specimen A specimen that is derived from some meconium Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent feces specimen collecting specimen from organism meconium UBERON_0007109 From 1780d09657c204417609bdfc05c076002b6a7739 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Mon, 16 Dec 2024 14:44:36 -0600 Subject: [PATCH 13/15] Convert most subClassOf axioms to EquivalentClass --- src/ontology/modules/specimens.owl | 418 +++++++++++++++------------ src/ontology/templates/specimens.tsv | 26 +- 2 files changed, 240 insertions(+), 204 deletions(-) diff --git a/src/ontology/modules/specimens.owl b/src/ontology/modules/specimens.owl index 2538379a..2d3ebfa7 100644 --- a/src/ontology/modules/specimens.owl +++ b/src/ontology/modules/specimens.owl @@ -536,13 +536,17 @@ - - - - - - - + + + + + + + + + + + cytoplasmic RNA extract Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.) @@ -557,19 +561,21 @@ - - - - - - - - - - - - - + + + + + + + + + + + + + + + RNA extract an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. @@ -590,13 +596,17 @@ - - - - - - - + + + + + + + + + + + total RNA extract Extraction of total RNA from cells with Qiagen mini RNeasy kit @@ -612,13 +622,17 @@ - - - - - - - + + + + + + + + + + + organellar RNA extract Extraction of organellar RNA from plant cells using organellar RNA binding protein. @@ -1125,13 +1139,17 @@ - - - - - - - + + + + + + + + + + + nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. @@ -1145,19 +1163,21 @@ - - - - - - - - - - - - - + + + + + + + + + + + + + + + DNA extract The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. @@ -3752,13 +3772,17 @@ - - - - - - - + + + + + + + + + + + A RNA extract that is the output of an extraction process in which RNA molecules lacking poly A tails at thier 3' ends are purified. Mark A. Miller, based on http://purl.obolibrary.org/obo/OBI_0000869 PERSON: Chris Stoeckert @@ -4337,29 +4361,31 @@ - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is collected with a suctioning tube from the trachea. Asiyah Yu Lin ORCID:0000-0003-2620-0345 tracheal wash specimen @@ -4722,27 +4748,29 @@ - - + + + + + + + + + + + + + + - - - - - + - - - - - - - + A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system. Chris Stoeckert Jie Zheng @@ -4800,37 +4828,39 @@ - - + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - + - - - - - - - + A specimen that is derived from part of a digestive tract. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB @@ -5964,29 +5994,31 @@ - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some erythrocytes Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066 @@ -6000,29 +6032,31 @@ - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some reticulocytes Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066 @@ -6036,29 +6070,31 @@ - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some leukocytes Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066 diff --git a/src/ontology/templates/specimens.tsv b/src/ontology/templates/specimens.tsv index 5ed3dc5b..ee60a076 100644 --- a/src/ontology/templates/specimens.tsv +++ b/src/ontology/templates/specimens.tsv @@ -9,10 +9,10 @@ OBI:0000834 high molecular weight DNA extract high molecular weight DNA extract OBI:0000862 nuclear RNA extract nuclear RNA extract metadata complete A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted. UPenn Group Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30) PERSON: Chris Stoeckert|PERSON: Jie Zheng subclass RNA extract nuclear RNA extraction OBI:0000869 polyA RNA extract polyA RNA extract metadata complete A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified. UPenn Group Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.) PERSON: Chris Stoeckert|PERSON: Jie Zheng subclass RNA extract polyA RNA extraction OBI:0000873 pre-mortem specimen pre-mortem specimen metadata complete a specimen that was taken from a live organism MO_705 premortem material obtained through a liver biopsy from a human patient Bjoern Peters equivalent specimen with pre- or post-mortem status ('organism' and ('has quality' some 'alive')) -OBI:0000876 cytoplasmic RNA extract cytoplasmic RNA extract metadata complete A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. UPenn Group Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.) PERSON:Chris Stoeckert subclass RNA extract cytoplasmic RNA extraction -OBI:0000880 RNA extract RNA extract metadata complete an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. Group: UPenn Group PERSON: Chris Stoeckert|PERSON: Jie Zheng subclass nucleic acid extract RNA extraction 'has grain' some 'ribonucleic acid' -OBI:0000895 total RNA extract total RNA extract metadata complete A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. UPenn Group Extraction of total RNA from cells with Qiagen mini RNeasy kit PERSON: Chris Stoeckert|PERSON: Jie Zheng subclass RNA extract total RNA extraction -OBI:0000899 organellar RNA extract organellar RNA extract metadata complete A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted. UPenn Group Extraction of organellar RNA from plant cells using organellar RNA binding protein. PERSON: Chris Stoeckert|PERSON: Jie Zheng subclass RNA extract organellar RNA extraction +OBI:0000876 cytoplasmic RNA extract cytoplasmic RNA extract metadata complete A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. UPenn Group Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.) PERSON:Chris Stoeckert equivalent RNA extract cytoplasmic RNA extraction +OBI:0000880 RNA extract RNA extract metadata complete an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. Group: UPenn Group PERSON: Chris Stoeckert|PERSON: Jie Zheng equivalent nucleic acid extract RNA extraction 'has grain' some 'ribonucleic acid' +OBI:0000895 total RNA extract total RNA extract metadata complete A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. UPenn Group Extraction of total RNA from cells with Qiagen mini RNeasy kit PERSON: Chris Stoeckert|PERSON: Jie Zheng equivalent RNA extract total RNA extraction +OBI:0000899 organellar RNA extract organellar RNA extract metadata complete A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted. UPenn Group Extraction of organellar RNA from plant cells using organellar RNA binding protein. PERSON: Chris Stoeckert|PERSON: Jie Zheng equivalent RNA extract organellar RNA extraction OBI:0000902 post mortem specimen post mortem specimen metadata complete a specimen that was taken from a dead organism MO_416 postmortem the spleen taken from a dead mouse Bjoern Peters equivalent specimen with pre- or post-mortem status ('organism' and ('has quality' some 'dead')) OBI:0000908 labeled DNA extract labeled DNA extract metadata complete a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. Group: OBI group Group: OBI group Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call equivalent labeled nucleic acid extract ('addition of molecular label' and ('has_specified_input' some 'DNA extract')) 'has grain' some 'deoxyribonucleic acid' OBI:0000909 cloacal specimen cell specimen metadata complete A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium. WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf type of sample used in the PCIRN influenza network PERSON: Melanie Courtot equivalent specimen from organism collecting specimen from organism cloaca @@ -26,8 +26,8 @@ OBI:0000953 processed specimen processed specimen ready for release A specimen OBI:0000965 lyophilized specimen lyophilized specimen metadata incomplete a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. MO_589 freeze_dried_sample freezing dried DNA PERSON: Chris Stoeckert|PERSON: Jie Zheng equivalent specimen ('lyophilization storage' and ('has_specified_input' some ('has role' some 'specimen role'))) OBI:0000971 fresh specimen fresh specimen metadata incomplete a specimen that is output of a specimen creation process used for an investigation without storage. MO_730 fresh_sample a liver freshly removed from a rat PERSON: Chris Stoeckert|PERSON: Jie Zheng subclass specimen with known storage state OBI:0000981 agar stab specimen agar stab specimen metadata incomplete a specimen that is output of a process that cell culture inoculated into agar for long term storage. MO_971 agar_stab PERSON: Chris Stoeckert|PERSON: Jie Zheng equivalent specimen ('agar stab storage' and ('has_specified_input' some ('has role' some 'specimen role'))) -OBI:0001010 nucleic acid extract nucleic acid extract metadata complete An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. UPenn Group Person: Jie Zheng subclass specimen nucleic acid extraction -OBI:0001051 DNA extract DNA extract metadata complete The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. Group: UPenn group Person: Jie Zheng subclass nucleic acid extract DNA extraction 'has grain' some 'deoxyribonucleic acid' +OBI:0001010 nucleic acid extract nucleic acid extract metadata complete An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. UPenn Group Person: Jie Zheng equivalent specimen nucleic acid extraction +OBI:0001051 DNA extract DNA extract metadata complete The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. Group: UPenn group Person: Jie Zheng equivalent nucleic acid extract DNA extraction 'has grain' some 'deoxyribonucleic acid' OBI:0001143 labeled nucleic acid extract labeled nucleic acid extract metadata complete labeled extract a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments. MO_221 labeledExtract Person: Jie Zheng equivalent labeled specimen ('addition of molecular label' and ('has_specified_input' some 'nucleic acid extract')) 'has grain' some 'nucleic acid' OBI:0001468 cell specimen cell specimen metadata incomplete A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture. MO_612 cell PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828 equivalent specimen from organism 'has part' some 'cell' OBI:0001472 specimen with known storage state specimen with known storage state metadata incomplete A specimen for which it is known whether it has been subjected to storage of a specified type. MO_95 BiosourceType PERSON: Chris Stoeckert, Jie Zheng equivalent specimen 'fresh specimen' or ('specimen' and ('is_specified_output_of' some 'storage')) @@ -91,7 +91,7 @@ OBI:0002551 suprapubic skin specimen ready for release A specimen that is deri OBI:0002552 testis specimen ready for release A specimen that is derived from testis. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some testis)) UBERON_0000473 OBI:0002553 uterus specimen ready for release A specimen that is derived from uterus. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some uterus)) UBERON_0000995 OBI:0002554 vagina specimen ready for release A specimen that is derived from vagina. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some vagina)) UBERON_0000996 -OBI:0002573 polyA depleted RNA extract A RNA extract that is the output of an extraction process in which RNA molecules lacking poly A tails at thier 3' ends are purified. UPenn Group PERSON: Chris Stoeckert|PERSON: Jie Zheng|Mark A. Miller, based on http://purl.obolibrary.org/obo/OBI_0000869 subclass RNA extract RNA extraction with polyA depletion +OBI:0002573 polyA depleted RNA extract A RNA extract that is the output of an extraction process in which RNA molecules lacking poly A tails at thier 3' ends are purified. UPenn Group PERSON: Chris Stoeckert|PERSON: Jie Zheng|Mark A. Miller, based on http://purl.obolibrary.org/obo/OBI_0000869 equivalent RNA extract RNA extraction with polyA depletion OBI:0002599 swab specimen swab specimen ready for release A specimen that is stored on a swab as the output of a collecting specimen with swab process. OBIB/OBI Chris Stoeckert OBIB https://github.com/obi-ontology/obi/issues/910 equivalent specimen collecting specimen with swab OBI:0002603 areolar swab specimen ready for release A specimen that is collected with a swab from the surface of an areola of a breast. Chris Stoeckert, OBIB Chris Stoeckert equivalent breast swab specimen collecting specimen with swab areola UBERON_0002032 OBI:0002604 breast swab specimen ready for release A specimen that is collected with a swab from the surface of a breast. Chris Stoeckert, OBIB Chris Stoeckert equivalent breast specimen collecting specimen with swab breast UBERON_0000310 @@ -109,7 +109,7 @@ OBI:0002648 individual organism specimen A specimen composed of an individual OBI:0002691 arthropod meal of blood specimen metadata complete blood meal A specimen of the blood ingested by an arthropod. VEuPathDB A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito. Chris Stoeckert|Jie Zheng The mosquito feeds on a human for example, ingests the blood of the human, this blood is then taken from the tummy of a mosquito and a PCR may be run on this specimen to identify that the mosquito definitely fed on a human. VEuPathDB https://github.com/obi-ontology/obi/issues/1117 subclass blood specimen collecting specimen from organism OBI:0002746 induced sputum specimen A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. PMC3297553 John Judkins subclass sputum specimen collecting specimen from organism sputum UBERON_0007311 OBI:0002774 platelet-poor plasma specimen A blood plasma specimen that is the output of some platelet-poor plasma preparation and is the portion of plasma that contains fewer than 10,000 platelets per microliter. PERSON: Matthew Diller subclass blood plasma specimen -OBI:0002778 tracheal aspirate specimen tracheal wash specimen A specimen that is collected with a suctioning tube from the trachea. PMID:25338241 Asiyah Yu Lin ORCID:0000-0003-2620-0345 subclass lower respiratory tract specimen aspiration specimen collection trachea UBERON_0003126 +OBI:0002778 tracheal aspirate specimen tracheal wash specimen A specimen that is collected with a suctioning tube from the trachea. PMID:25338241 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent lower respiratory tract specimen aspiration specimen collection trachea UBERON_0003126 OBI:0002779 mid-turbinate nasal swab specimen A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity. https://seattlechildrenslab.testcatalog.org/catalogs/185/files/11633 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent nasal swab specimen collecting specimen with swab middle nasal concha UBERON_0005921 OBI:0002780 nasal aspirate specimen nasal wash specimen|nasopharyngeal aspirate A specimen that is collected with a suctioning tube from the nasal cavity. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent upper respiratory tract specimen aspiration specimen collection nasal cavity mucosa UBERON_0001826 OBI:0002781 lower respiratory tract aspirate specimen lower respiratory tract wash specimen A specimen that is collected with a suctioning tube from the lower respiratory tract. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent lower respiratory tract specimen aspiration specimen collection lower respiratory tract UBERON_0001558 @@ -120,9 +120,9 @@ OBI:0002972 endotracheal aspirate specimen A specimen that derives from a bio OBI:0003054 blood specimen in vacutainer Vacutainer sample A blood specimen that is located in a vacutainer. VEuPathDB John Judkins subclass blood specimen collecting specimen from organism blood UBERON_0000178 OBI:0003055 blood specimen on filter paper Filter paper sample A blood specimen that is located on a filter paper. Penn Group Jie Zheng|Chris Stoeckert subclass blood specimen collecting specimen from organism blood UBERON_0000178 OBI:0003380 placental blood specimen A specimen that is derived from placental blood. VEuPathDB John Judkins equivalent blood specimen collecting specimen from organism placental blood UBERON_8470000 -OBI:0003415 peripheral blood mononuclear cell specimen PBMC specimen A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system. http://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell Jie Zheng|Chris Stoeckert subclass blood specimen collecting specimen from organism peripheral blood mononuclear cell CL_2000001 +OBI:0003415 peripheral blood mononuclear cell specimen PBMC specimen A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system. http://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell Jie Zheng|Chris Stoeckert equivalent blood specimen collecting specimen from organism peripheral blood mononuclear cell CL_2000001 OBI:0003482 lymph specimen A specimen that is derived from a portion of lymph collected from an organism. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 equivalent bodily fluid specimen collecting specimen from organism (tissue and ('part of' some lymph)) UBERON_0002391 -OBI:0003483 digestive tract specimen A specimen that is derived from part of a digestive tract. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 specimen from organism collecting specimen from organism (tissue and ('part of' some 'digestive tract')) UBERON_0001555 +OBI:0003483 digestive tract specimen A specimen that is derived from part of a digestive tract. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'digestive tract')) UBERON_0001555 OBI:0003595 nasal lavage fluid A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space. Sebastian Duesing|Randi Vita equivalent lavage fluid specimen lavage nasal cavity mucosa UBERON_0001826 OBI:0003652 albumin-free serum albumin-free serum A blood serum specimen that contains no albumin. Sebastian Duesing Philippe Rocca-Serra https://github.com/obi-ontology/obi/issues/493 equivalent blood serum specimen 'has part' only (not ('albumin')) OBI:0003666 lavage fluid specimen lavage fluid specimen A specimen obtained through a lavage process which includes fluid in addition to cells and/or cellular secretions. The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1803 equivalent specimen from organism lavage @@ -151,6 +151,6 @@ OBI:2000012 umbilical cord blood specimen A specimen that is derived from som OBI:2000013 arterial blood specimen A specimen that is derived from some arterial blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent blood specimen collecting specimen from organism arterial blood UBERON_0013755 OBI:2000014 venous blood specimen A specimen that is derived from some venous blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent blood specimen collecting specimen from organism venous blood UBERON_0013756 OBI:2000015 capillary blood specimen A specimen that is derived from some capillary blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent blood specimen collecting specimen from organism capillary blood UBERON_0013757 -OBI:2000016 erythrocyte specimen A specimen that is derived from some erythrocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X subclass specimen from organism collecting specimen with swab erythrocyte CL_0000232 -OBI:2000017 reticulocyte specimen A specimen that is derived from some reticulocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X subclass specimen from organism collecting specimen with swab reticulocyte CL_0000558 -OBI:2000018 leukocyte specimen A specimen that is derived from some leukocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X subclass specimen from organism collecting specimen with swab leukocyte CL_0000738 +OBI:2000016 erythrocyte specimen A specimen that is derived from some erythrocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen with swab erythrocyte CL_0000232 +OBI:2000017 reticulocyte specimen A specimen that is derived from some reticulocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen with swab reticulocyte CL_0000558 +OBI:2000018 leukocyte specimen A specimen that is derived from some leukocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen with swab leukocyte CL_0000738 From fbc571bd1f1cc6584b11935711b8f67862b621aa Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Mon, 16 Dec 2024 14:54:05 -0600 Subject: [PATCH 14/15] Improve consistency of the axioms for aspiration specimens --- src/ontology/modules/specimens.owl | 4 ++-- src/ontology/templates/specimens.tsv | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/ontology/modules/specimens.owl b/src/ontology/modules/specimens.owl index 2d3ebfa7..7cc2f027 100644 --- a/src/ontology/modules/specimens.owl +++ b/src/ontology/modules/specimens.owl @@ -787,7 +787,7 @@ - + nasopharyngeal aspirate specimen @@ -4633,7 +4633,7 @@ - + A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube. diff --git a/src/ontology/templates/specimens.tsv b/src/ontology/templates/specimens.tsv index ee60a076..9e203296 100644 --- a/src/ontology/templates/specimens.tsv +++ b/src/ontology/templates/specimens.tsv @@ -16,7 +16,7 @@ OBI:0000899 organellar RNA extract organellar RNA extract metadata complete A R OBI:0000902 post mortem specimen post mortem specimen metadata complete a specimen that was taken from a dead organism MO_416 postmortem the spleen taken from a dead mouse Bjoern Peters equivalent specimen with pre- or post-mortem status ('organism' and ('has quality' some 'dead')) OBI:0000908 labeled DNA extract labeled DNA extract metadata complete a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. Group: OBI group Group: OBI group Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call equivalent labeled nucleic acid extract ('addition of molecular label' and ('has_specified_input' some 'DNA extract')) 'has grain' some 'deoxyribonucleic acid' OBI:0000909 cloacal specimen cell specimen metadata complete A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium. WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf type of sample used in the PCIRN influenza network PERSON: Melanie Courtot equivalent specimen from organism collecting specimen from organism cloaca -OBI:0000914 nasopharyngeal aspirate specimen nasopharyngeal aspirate specimen metadata complete A specimen which derives from nasopharyngeal mucosa after aspiration. WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf type of sample used in the PCIRN influenza network PERSON: Melanie Courtot subclass nasopharynx specimen collecting specimen from organism nasopharynx +OBI:0000914 nasopharyngeal aspirate specimen nasopharyngeal aspirate specimen metadata complete A specimen which derives from nasopharyngeal mucosa after aspiration. WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf type of sample used in the PCIRN influenza network PERSON: Melanie Courtot subclass nasopharynx specimen aspiration specimen collection nasopharynx OBI:0000917 nasal swab specimen nasal swab specimen metadata complete A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination. WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf type of sample used in the PCIRN influenza network PERSON: Melanie Courtot equivalent upper respiratory tract specimen collecting specimen with swab nasal cavity mucosa OBI:0000921 labeled RNA extract labeled RNA extract metadata complete a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments. Group: OBI group Group: OBI group Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call equivalent labeled nucleic acid extract ('addition of molecular label' and ('has_specified_input' some 'RNA extract')) 'has grain' some 'ribonucleic acid' OBI:0000922 frozen specimen frozen specimen metadata incomplete A specimen that has been frozen in order to store it. MO_610 frozen_sample Frozen blood plasma Person:Alan Ruttenberg equivalent specimen ('freezing storage' and ('has_specified_input' some ('has role' some 'specimen role'))) @@ -116,7 +116,7 @@ OBI:0002781 lower respiratory tract aspirate specimen lower respiratory tract OBI:0002783 lower respiratory tract specimen A specimen that is derived from the lower respiratory tract. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent respiratory system specimen lower respiratory tract UBERON_0001558 OBI:0002784 anterior nasal swab specimen A specimen that is derived from the anterior nasal wall Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 equivalent nasal swab specimen collecting specimen with swab anterior nasal wall UBERON_3000016 OBI:0002971 endotracheal tube specimen A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea. https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 John Judkins ORCID:0000-0001-6595-0902 subclass lower respiratory tract specimen collecting specimen from organism respiratory system fluid/secretion UBERON_0006538 -OBI:0002972 endotracheal aspirate specimen A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube. https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 John Judkins ORCID:0000-0001-6595-0902 subclass lower respiratory tract specimen collecting specimen from organism respiratory system fluid/secretion UBERON_0006538 +OBI:0002972 endotracheal aspirate specimen A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube. https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 John Judkins ORCID:0000-0001-6595-0902 subclass lower respiratory tract specimen aspiration specimen collection respiratory system fluid/secretion UBERON_0006538 OBI:0003054 blood specimen in vacutainer Vacutainer sample A blood specimen that is located in a vacutainer. VEuPathDB John Judkins subclass blood specimen collecting specimen from organism blood UBERON_0000178 OBI:0003055 blood specimen on filter paper Filter paper sample A blood specimen that is located on a filter paper. Penn Group Jie Zheng|Chris Stoeckert subclass blood specimen collecting specimen from organism blood UBERON_0000178 OBI:0003380 placental blood specimen A specimen that is derived from placental blood. VEuPathDB John Judkins equivalent blood specimen collecting specimen from organism placental blood UBERON_8470000 From c2bfa225065d36f16213a4c1ea23d95b2c85741e Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Mon, 6 Jan 2025 11:52:46 -0600 Subject: [PATCH 15/15] Fix wrong collection method in blood cell specimens --- src/ontology/modules/specimens.owl | 12 ++++++------ src/ontology/templates/specimens.tsv | 6 +++--- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/ontology/modules/specimens.owl b/src/ontology/modules/specimens.owl index 7cc2f027..2201d562 100644 --- a/src/ontology/modules/specimens.owl +++ b/src/ontology/modules/specimens.owl @@ -5997,10 +5997,10 @@ - + - + @@ -6035,10 +6035,10 @@ - + - + @@ -6073,10 +6073,10 @@ - + - + diff --git a/src/ontology/templates/specimens.tsv b/src/ontology/templates/specimens.tsv index 9e203296..e8530df7 100644 --- a/src/ontology/templates/specimens.tsv +++ b/src/ontology/templates/specimens.tsv @@ -151,6 +151,6 @@ OBI:2000012 umbilical cord blood specimen A specimen that is derived from som OBI:2000013 arterial blood specimen A specimen that is derived from some arterial blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent blood specimen collecting specimen from organism arterial blood UBERON_0013755 OBI:2000014 venous blood specimen A specimen that is derived from some venous blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent blood specimen collecting specimen from organism venous blood UBERON_0013756 OBI:2000015 capillary blood specimen A specimen that is derived from some capillary blood Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent blood specimen collecting specimen from organism capillary blood UBERON_0013757 -OBI:2000016 erythrocyte specimen A specimen that is derived from some erythrocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen with swab erythrocyte CL_0000232 -OBI:2000017 reticulocyte specimen A specimen that is derived from some reticulocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen with swab reticulocyte CL_0000558 -OBI:2000018 leukocyte specimen A specimen that is derived from some leukocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent specimen from organism collecting specimen with swab leukocyte CL_0000738 +OBI:2000016 erythrocyte specimen A specimen that is derived from some erythrocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent cell specimen collecting specimen from organism erythrocyte CL_0000232 +OBI:2000017 reticulocyte specimen A specimen that is derived from some reticulocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent cell specimen collecting specimen from organism reticulocyte CL_0000558 +OBI:2000018 leukocyte specimen A specimen that is derived from some leukocytes Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent cell specimen collecting specimen from organism leukocyte CL_0000738