From 9a79b628b4fd8c7ac06ca3f7de0b7e9525cb71bb Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 8 Oct 2024 18:44:15 -0500 Subject: [PATCH] Add column to template for parent and add more classes to template --- src/ontology/modules/biobank-specimens.owl | 3431 +++++++++--------- src/ontology/obi-edit.owl | 733 +--- src/ontology/templates/biobank-specimens.tsv | 264 +- 3 files changed, 1914 insertions(+), 2514 deletions(-) diff --git a/src/ontology/modules/biobank-specimens.owl b/src/ontology/modules/biobank-specimens.owl index bfa24c30..2698294f 100644 --- a/src/ontology/modules/biobank-specimens.owl +++ b/src/ontology/modules/biobank-specimens.owl @@ -117,6 +117,24 @@ + + + + + + + + + + + + + + + + + + @@ -140,6 +158,24 @@ + + + + + + + + + + + + + + + + + + @@ -176,15 +212,27 @@ + + + + + + + + + + + + + - @@ -195,15 +243,10 @@ - - - - - - - - - + + + + @@ -218,15 +261,21 @@ + + + + + + + - @@ -237,15 +286,10 @@ - - - - - - - - - + + + + @@ -266,15 +310,150 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + pre-mortem specimen + material obtained through a liver biopsy from a human patient + + a specimen that was taken from a live organism + Bjoern Peters + MO_705 premortem + pre-mortem specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + post mortem specimen + the spleen taken from a dead mouse + + a specimen that was taken from a dead organism + Bjoern Peters + MO_416 postmortem + post mortem specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + labeled DNA extract + + 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. + 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 + Group: OBI group + Group: OBI group + labeled DNA extract + + + + + - @@ -285,15 +464,10 @@ - - - - - - - - - + + + + @@ -311,10 +485,10 @@ + - @@ -327,15 +501,10 @@ - - - - - - - - - + + + + nasopharyngeal aspirate specimen type of sample used in the PCIRN influenza network @@ -348,40 +517,37 @@ + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -396,73 +562,537 @@ - + - + - + - - + + + + + + + + + + + + + + + + - cell specimen - - A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture. - 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 - PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl - MO_612 cell - cell specimen - - - - - - - - + labeled RNA extract - A cell specimen that contains only one cell. - Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/ - PERSON: Jie Zheng, Alexander Diehl - PERSON: Jie Zheng, Alexander Diehl - single cell specimen + 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. + 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 + Group: OBI group + Group: OBI group + labeled RNA extract - + - + - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + frozen specimen + Frozen blood plasma + + A specimen that has been frozen in order to store it. + Person:Alan Ruttenberg + MO_610 frozen_sample + frozen specimen + + + + + + + + + + + + + + + + + + + + + + + labeled specimen + + A specimen that has been modified in order to be able to detect it in future experiments + added during call 3/1/2010 + OBI group + labeled specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + paraffin specimen + liver tissue embedded in paraffin + + a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin + PERSON: Chris Stoeckert + PERSON: Jie Zheng + MO_990 paraffin_sample + paraffin specimen + + + + + + + + + + + + + + + + + + + processed specimen + + A specimen that has been intentionally physically modified. + A tissue sample that has been sliced and stained for a histology study. + Bjoern Peters + Bjoern Peters + processed specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + lyophilized specimen + freezing dried DNA + + a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + MO_589 freeze_dried_sample + lyophilized specimen + + + + + + + + + fresh specimen + a liver freshly removed from a rat + + a specimen that is output of a specimen creation process used for an investigation without storage. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + MO_730 fresh_sample + fresh specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + agar stab specimen + + a specimen that is output of a process that cell culture inoculated into agar for long term storage. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + MO_971 agar_stab + agar stab specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + labeled nucleic acid 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. + Person: Jie Zheng + labeled extract + MO_221 labeledExtract + labeled nucleic acid extract + + + + + + + + + + + + + + + + + + + cell specimen + + A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture. + 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 + PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl + MO_612 cell + cell specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + specimen with known storage state + + A specimen for which it is known whether it has been subjected to storage of a specified type. + PERSON: Chris Stoeckert, Jie Zheng + MO_95 BiosourceType + specimen with known storage state + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). + PERSON: Chris Stoeckert, Jie Zheng + tissue specimen + MO_954 organism_part + specimen from organism + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + specimen with pre- or post-mortem status + + A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. + organizational term, used in description of specimen that is created from known pre- or post-mortem status + PERSON: Chris Stoeckert, Jie Zheng + MO_84 OrganismStatus + specimen with pre- or post-mortem status + + + + + + + + + + A cell specimen that contains only one cell. + Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/ + PERSON: Jie Zheng, Alexander Diehl + PERSON: Jie Zheng, Alexander Diehl + single cell specimen + + + + + + + + + + + - - + + + + + + + + + @@ -481,9 +1111,9 @@ + - @@ -494,15 +1124,10 @@ - - - - - - - - - + + + + @@ -521,9 +1146,9 @@ + - @@ -534,15 +1159,10 @@ - - - - - - - - - + + + + @@ -561,9 +1181,9 @@ + - @@ -574,15 +1194,10 @@ - - - - - - - - - + + + + @@ -602,9 +1217,9 @@ + - @@ -615,15 +1230,10 @@ - - - - - - - - - + + + + @@ -643,9 +1253,9 @@ + - @@ -656,15 +1266,10 @@ - - - - - - - - - + + + + @@ -683,9 +1288,9 @@ + - @@ -696,15 +1301,10 @@ - - - - - - - - - + + + + @@ -723,9 +1323,9 @@ + - @@ -736,15 +1336,10 @@ - - - - - - - - - + + + + @@ -763,9 +1358,9 @@ + - @@ -776,15 +1371,10 @@ - - - - - - - - - + + + + @@ -803,28 +1393,23 @@ + - - - - - - - - - - - - - - - + + + + + + + + + @@ -843,9 +1428,9 @@ + - @@ -856,15 +1441,10 @@ - - - - - - - - - + + + + @@ -883,9 +1463,9 @@ + - @@ -906,15 +1486,10 @@ - - - - - - - - - + + + + @@ -934,9 +1509,9 @@ + - @@ -947,15 +1522,10 @@ - - - - - - - - - + + + + @@ -974,9 +1544,9 @@ + - @@ -997,15 +1567,10 @@ - - - - - - - - - + + + + @@ -1024,9 +1589,9 @@ + - @@ -1037,15 +1602,10 @@ - - - - - - - - - + + + + @@ -1064,9 +1624,9 @@ + - @@ -1077,15 +1637,10 @@ - - - - - - - - - + + + + @@ -1104,9 +1659,9 @@ + - @@ -1127,15 +1682,10 @@ - - - - - - - - - + + + + @@ -1154,9 +1704,9 @@ + - @@ -1167,15 +1717,10 @@ - - - - - - - - - + + + + @@ -1194,9 +1739,9 @@ + - @@ -1217,15 +1762,10 @@ - - - - - - - - - + + + + @@ -1244,9 +1784,9 @@ + - @@ -1257,15 +1797,10 @@ - - - - - - - - - + + + + @@ -1284,9 +1819,9 @@ + - @@ -1307,15 +1842,10 @@ - - - - - - - - - + + + + @@ -1334,9 +1864,9 @@ + - @@ -1357,15 +1887,10 @@ - - - - - - - - - + + + + @@ -1385,9 +1910,9 @@ + - @@ -1408,15 +1933,10 @@ - - - - - - - - - + + + + @@ -1435,9 +1955,9 @@ + - @@ -1458,15 +1978,10 @@ - - - - - - - - - + + + + @@ -1486,9 +2001,9 @@ + - @@ -1509,15 +2024,10 @@ - - - - - - - - - + + + + @@ -1536,9 +2046,9 @@ + - @@ -1559,15 +2069,10 @@ - - - - - - - - - + + + + @@ -1586,9 +2091,9 @@ + - @@ -1609,15 +2114,10 @@ - - - - - - - - - + + + + @@ -1637,9 +2137,9 @@ + - @@ -1660,15 +2160,10 @@ - - - - - - - - - + + + + @@ -1687,9 +2182,9 @@ + - @@ -1710,15 +2205,10 @@ - - - - - - - - - + + + + @@ -1737,9 +2227,9 @@ + - @@ -1760,15 +2250,10 @@ - - - - - - - - - + + + + @@ -1787,9 +2272,9 @@ + - @@ -1800,15 +2285,10 @@ - - - - - - - - - + + + + @@ -1827,9 +2307,9 @@ + - @@ -1850,15 +2330,10 @@ - - - - - - - - - + + + + @@ -1878,9 +2353,9 @@ + - @@ -1901,15 +2376,10 @@ - - - - - - - - - + + + + @@ -1928,9 +2398,9 @@ + - @@ -1951,15 +2421,10 @@ - - - - - - - - - + + + + @@ -1978,9 +2443,9 @@ + - @@ -2001,15 +2466,10 @@ - - - - - - - - - + + + + @@ -2028,9 +2488,9 @@ + - @@ -2051,15 +2511,10 @@ - - - - - - - - - + + + + @@ -2079,9 +2534,9 @@ + - @@ -2102,15 +2557,10 @@ - - - - - - - - - + + + + @@ -2130,9 +2580,9 @@ + - @@ -2153,15 +2603,10 @@ - - - - - - - - - + + + + @@ -2180,9 +2625,9 @@ + - @@ -2203,15 +2648,10 @@ - - - - - - - - - + + + + @@ -2231,9 +2671,9 @@ + - @@ -2254,15 +2694,10 @@ - - - - - - - - - + + + + @@ -2281,9 +2716,9 @@ + - @@ -2304,15 +2739,10 @@ - - - - - - - - - + + + + @@ -2331,9 +2761,9 @@ + - @@ -2354,15 +2784,10 @@ - - - - - - - - - + + + + @@ -2381,9 +2806,9 @@ + - @@ -2404,15 +2829,10 @@ - - - - - - - - - + + + + @@ -2431,9 +2851,9 @@ + - @@ -2454,15 +2874,10 @@ - - - - - - - - - + + + + @@ -2481,9 +2896,9 @@ + - @@ -2504,15 +2919,10 @@ - - - - - - - - - + + + + @@ -2531,9 +2941,9 @@ + - @@ -2554,15 +2964,10 @@ - - - - - - - - - + + + + @@ -2581,9 +2986,9 @@ + - @@ -2604,15 +3009,10 @@ - - - - - - - - - + + + + @@ -2631,9 +3031,9 @@ + - @@ -2654,15 +3054,10 @@ - - - - - - - - - + + + + @@ -2681,9 +3076,9 @@ + - @@ -2704,15 +3099,10 @@ - - - - - - - - - + + + + @@ -2731,9 +3121,9 @@ + - @@ -2754,15 +3144,10 @@ - - - - - - - - - + + + + @@ -2781,9 +3166,9 @@ + - @@ -2804,15 +3189,10 @@ - - - - - - - - - + + + + @@ -2831,9 +3211,9 @@ + - @@ -2854,15 +3234,10 @@ - - - - - - - - - + + + + @@ -2881,9 +3256,9 @@ + - @@ -2904,15 +3279,10 @@ - - - - - - - - - + + + + @@ -2931,9 +3301,9 @@ + - @@ -2954,15 +3324,10 @@ - - - - - - - - - + + + + @@ -2981,9 +3346,9 @@ + - @@ -3004,15 +3369,10 @@ - - - - - - - - - + + + + @@ -3025,6 +3385,32 @@ + + + + + + + + + + + + + + + swab specimen + + A specimen that is stored on a swab as the output of a collecting specimen with swab process. + Chris Stoeckert + OBIB/OBI + https://github.com/obi-ontology/obi/issues/910 + OBIB + swab specimen + + + + @@ -3037,34 +3423,25 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -3083,34 +3460,25 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -3129,34 +3497,25 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -3175,34 +3534,25 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -3221,34 +3571,25 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -3267,34 +3608,25 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -3313,34 +3645,25 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -3359,34 +3682,25 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -3405,80 +3719,62 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + - - - - A specimen that is collected with a swab from the surface of a vagina. - Chris Stoeckert - Chris Stoeckert, OBIB - vagina swab specimen - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + A specimen that is collected with a swab from the surface of a vagina. + Chris Stoeckert + Chris Stoeckert, OBIB + vagina swab specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -3498,34 +3794,25 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -3571,16 +3858,12 @@ + - - - - - - - - - + + + + A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito. @@ -3597,13 +3880,19 @@ + + + + + + + - @@ -3616,15 +3905,10 @@ - - - - - - - - - + + + + A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. John Judkins @@ -3648,37 +3932,28 @@ + - - - - - - - - - + + + + - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + A specimen that is collected with a suctioning tube from the trachea. Asiyah Yu Lin ORCID:0000-0003-2620-0345 @@ -3695,34 +3970,25 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -3740,34 +4006,25 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -3787,34 +4044,25 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -3833,34 +4081,25 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -3878,7 +4117,7 @@ - + @@ -3910,34 +4149,25 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -3958,10 +4188,10 @@ + - @@ -3974,15 +4204,10 @@ - - - - - - - - - + + + + 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. John Judkins ORCID:0000-0001-6595-0902 @@ -3995,10 +4220,10 @@ + - @@ -4011,15 +4236,10 @@ - - - - - - - - - + + + + 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. John Judkins ORCID:0000-0001-6595-0902 @@ -4032,10 +4252,10 @@ + - @@ -4048,15 +4268,10 @@ - - - - - - - - - + + + + A blood specimen that is located in a vacutainer. John Judkins @@ -4070,10 +4285,10 @@ + - @@ -4086,15 +4301,10 @@ - - - - - - - - - + + + + A blood specimen that is located on a filter paper. Chris Stoeckert @@ -4112,9 +4322,9 @@ + - @@ -4125,15 +4335,10 @@ - - - - - - - - - + + + + @@ -4148,10 +4353,10 @@ + - @@ -4164,15 +4369,10 @@ - - - - - - - - - + + + + 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 @@ -4187,10 +4387,10 @@ + - @@ -4213,15 +4413,10 @@ - - - - - - - - - + + + + A specimen that is derived from a portion of lymph collected from an organism. John Judkins ORCID:0000-0001-6595-0902 @@ -4234,10 +4429,10 @@ + - @@ -4260,15 +4455,10 @@ - - - - - - - - - + + + + A specimen that is derived from part of a digestive tract. John Judkins ORCID:0000-0001-6595-0902 @@ -4284,34 +4474,25 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -4357,89 +4538,44 @@ - - - - - - - - - lavage fluid specimen - The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present. - A specimen obtained through a lavage process which includes fluid in addition to cells and/or cellular secretions. - Sebastian Duesing - https://github.com/obi-ontology/obi/issues/1803 - lavage fluid specimen - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - oral lavage fluid - A specimen collected through oral cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the oral cavity space. + lavage fluid specimen + The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present. + A specimen obtained through a lavage process which includes fluid in addition to cells and/or cellular secretions. Sebastian Duesing - mouth rinse specimen https://github.com/obi-ontology/obi/issues/1803 - Anna Maria Masci - oral lavage fluid + lavage fluid specimen - + - - - + + - + + + + + - + - + @@ -4447,6 +4583,37 @@ + + oral lavage fluid + A specimen collected through oral cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the oral cavity space. + Sebastian Duesing + mouth rinse specimen + https://github.com/obi-ontology/obi/issues/1803 + Anna Maria Masci + oral lavage fluid + + + + + + + + + + + + + + + + + + + + + + + blood plasma specimen PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings. @@ -4468,31 +4635,26 @@ - - - - - - + + + + + - - - - - - - - - - - - - + + + + + - - - - + + + + + + + + blood serum specimen PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy. @@ -4525,9 +4687,9 @@ + - @@ -4538,15 +4700,10 @@ - - - - - - - - - + + + + @@ -4562,6 +4719,41 @@ + + + + + + + + + + + + + + + + + + + + + + + + + pool of specimens + + A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. + check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish + PERSON: Jennifer Fostel + GROUP: CEBS + pool of specimens + + + + @@ -4574,6 +4766,12 @@ + + + + + + @@ -4586,6 +4784,12 @@ + + + + + + @@ -4605,25 +4809,20 @@ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + @@ -4650,25 +4849,20 @@ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + @@ -4688,9 +4882,9 @@ + - @@ -4711,15 +4905,10 @@ - - - - - - - - - + + + + @@ -4739,9 +4928,9 @@ + - @@ -4762,15 +4951,10 @@ - - - - - - - - - + + + + @@ -4790,9 +4974,9 @@ + - @@ -4803,15 +4987,10 @@ - - - - - - - - - + + + + @@ -4831,9 +5010,9 @@ + - @@ -4854,15 +5033,10 @@ - - - - - - - - - + + + + @@ -4882,9 +5056,9 @@ + - @@ -4905,15 +5079,10 @@ - - - - - - - - - + + + + @@ -4933,9 +5102,9 @@ + - @@ -4946,25 +5115,20 @@ - - - - - - - - - - - - - - - - + + + + + + + + + + + @@ -4984,9 +5148,9 @@ + - @@ -5007,15 +5171,10 @@ - - - - - - - - - + + + + @@ -5035,9 +5194,9 @@ + - @@ -5058,15 +5217,10 @@ - - - - - - - - - + + + + @@ -5086,9 +5240,9 @@ + - @@ -5099,15 +5253,10 @@ - - - - - - - - - + + + + @@ -5127,9 +5276,9 @@ + - @@ -5140,15 +5289,10 @@ - - - - - - - - - + + + + @@ -5168,9 +5312,9 @@ + - @@ -5191,15 +5335,10 @@ - - - - - - - - - + + + + @@ -5219,9 +5358,9 @@ + - @@ -5232,15 +5371,10 @@ - - - - - - - - - + + + + @@ -5260,9 +5394,9 @@ + - @@ -5273,15 +5407,10 @@ - - - - - - - - - + + + + @@ -5301,9 +5430,9 @@ + - @@ -5314,15 +5443,10 @@ - - - - - - - - - + + + + @@ -5342,9 +5466,9 @@ + - @@ -5355,15 +5479,10 @@ - - - - - - - - - + + + + @@ -5383,9 +5502,9 @@ + - @@ -5396,15 +5515,10 @@ - - - - - - - - - + + + + @@ -5421,37 +5535,28 @@ + - - - - - - - - - + + + + - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + A specimen that is derived from some erythrocytes Christian Stoeckert ORCID:0000-0002-5714-991X @@ -5466,37 +5571,28 @@ + - - - - - - - - - + + + + - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + A specimen that is derived from some reticulocytes Christian Stoeckert ORCID:0000-0002-5714-991X @@ -5511,37 +5607,28 @@ + - - - - - - - - - + + + + - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + A specimen that is derived from some leukocytes Christian Stoeckert ORCID:0000-0002-5714-991X @@ -5553,6 +5640,18 @@ + + + + + + + + + + + + @@ -5631,12 +5730,24 @@ + + + + + + + + + + + + diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 3438503c..780b734e 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -10106,48 +10106,6 @@ placeholder - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - pre-mortem specimen - material obtained through a liver biopsy from a human patient - - a specimen that was taken from a live organism - Bjoern Peters - MO_705 premortem - pre-mortem specimen - - - - @@ -10386,47 +10344,6 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - post mortem specimen - the spleen taken from a dead mouse - - a specimen that was taken from a dead organism - Bjoern Peters - MO_416 postmortem - post mortem specimen - - - - @@ -10488,52 +10405,6 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - labeled DNA extract - - 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. - 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 - Group: OBI group - Group: OBI group - labeled DNA extract - - - - @@ -10646,128 +10517,6 @@ Updated both textual and logical definition. Both input and output material of f - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - labeled RNA extract - - 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. - 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 - Group: OBI group - Group: OBI group - labeled RNA extract - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - frozen specimen - Frozen blood plasma - - A specimen that has been frozen in order to store it. - Person:Alan Ruttenberg - MO_610 frozen_sample - frozen specimen - - - - - - - - - - - - - - - - - - - - - - - labeled specimen - - A specimen that has been modified in order to be able to detect it in future experiments - added during call 3/1/2010 - OBI group - labeled specimen - - - - @@ -11052,78 +10801,6 @@ Biochimie. 2010 Feb 18. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - paraffin specimen - liver tissue embedded in paraffin - - a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin - PERSON: Chris Stoeckert - PERSON: Jie Zheng - MO_990 paraffin_sample - paraffin specimen - - - - - - - - - - - - - - - - processed specimen - A tissue sample that has been sliced and stained for a histology study. -A blood specimen that has been centrifuged to obtain the white blood cells. - - A specimen that has been intentionally physically modified. - Bjoern Peters - Bjoern Peters - A tissue sample that has been sliced and stained for a histology study. - processed specimen - - - - @@ -11180,54 +10857,7 @@ A blood specimen that has been centrifuged to obtain the white blood cells.A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. Bjoern Peters Bjoern Peters - categorical label - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - lyophilized specimen - freezing dried DNA - - a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - MO_589 freeze_dried_sample - lyophilized specimen + categorical label @@ -11325,23 +10955,6 @@ In the examples above, a reagent is an operational component of a device, but th - - - - - - fresh specimen - a liver freshly removed from a rat - - a specimen that is output of a specimen creation process used for an investigation without storage. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - MO_730 fresh_sample - fresh specimen - - - - @@ -11437,42 +11050,6 @@ In the examples above, a reagent is an operational component of a device, but th - - - - - - - - - - - - - - - - - - - - - - - - - - agar stab specimen - - a specimen that is output of a process that cell culture inoculated into agar for long term storage. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - MO_971 agar_stab - agar stab specimen - - - - @@ -11969,52 +11546,6 @@ JZ: based on textual definition of edited document, it can be defined as N&S - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - labeled nucleic acid 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. - Person: Jie Zheng - labeled extract - MO_221 labeledExtract - labeled extract - labeled nucleic acid extract - - - - @@ -13758,36 +13289,6 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - - - - - - - - - - - - - specimen with known storage state - - A specimen for which it is known whether it has been subjected to storage of a specified type. - PERSON: Chris Stoeckert, Jie Zheng - MO_95 BiosourceType - specimen with known storage state - - - - @@ -13822,65 +13323,6 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). - PERSON: Chris Stoeckert, Jie Zheng - tissue specimen - MO_954 organism_part - specimen from organism - - - - @@ -14164,54 +13606,6 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - specimen with pre- or post-mortem status - - A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. - organizational term, used in description of specimen that is created from known pre- or post-mortem status - PERSON: Chris Stoeckert, Jie Zheng - MO_84 OrganismStatus - specimen with pre- or post-mortem status - - - - @@ -18644,55 +18038,6 @@ https://www.doi.org/ - - - - - - - - - - - - - - - H&E-stained fixed tissue slide specimen - - A fixed tissue slide specimen that is the output of H&E slide staining. - Chris Stoeckert, Ned Haubein - OBIB, OBI - H&E-stained fixed tissue slide specimen - - - - - - - - - - - - - - - - - - - IHC-stained fixed tissue slide specimen - - A fixed tissue slide specimen that is the output of immunohistochemistry slide staining. - Chris Stoeckert, Ned Haubein - immunohistochemistry slide specimen - OBIB, OBI - IHC-stained fixed tissue slide specimen - - - - @@ -19582,28 +18927,6 @@ https://www.doi.org/ - - - - - - - - - - - swab specimen - - A specimen that is stored on a swab as the output of a collecting specimen with swab process. - Chris Stoeckert - OBIB/OBI - https://github.com/obi-ontology/obi/issues/910 - OBIB - swab specimen - - - - @@ -26178,42 +25501,6 @@ determinations of compounds. - - - - - - - - - - - - - - - - - - - - - - - - - - pool of specimens - - A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. - check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish - PERSON: Jennifer Fostel - GROUP: CEBS - pool of specimens - - - - @@ -31442,24 +30729,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - FFPE specimen - 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/ - A specimen that has been fixed in formalin and embedded in paraffin. - MIABIS - formalin-fixed paraffin-embeded specimen - - - FFPE specimen - - - - diff --git a/src/ontology/templates/biobank-specimens.tsv b/src/ontology/templates/biobank-specimens.tsv index 9903b496..7ddbf439 100644 --- a/src/ontology/templates/biobank-specimens.tsv +++ b/src/ontology/templates/biobank-specimens.tsv @@ -1,122 +1,142 @@ -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 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 specimen and (is_specified_output_of some %) C specimen and (is_specified_output_of some 'specimen collection process') and ('derives from' some %) C specimen and (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 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 collecting specimen from organism blood -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 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 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 collecting specimen with swab nasal cavity mucosa -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' and ('has part' some 'cell') -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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 collecting specimen from organism (tissue and ('part of' some 'prostate gland')) UBERON_0002367 -OBI:0002519 skeletal muscle tissue specimen ready for release A specimen that is derived from skeletal muscle. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism skeletal muscle tissue UBERON_0001134 -OBI:0002520 heart specimen ready for release A specimen that is derived from heart. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some heart)) UBERON_0000948 -OBI:0002521 renal medulla specimen ready for release kidney medulla specimen A specimen that is derived from renal medulla. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'renal medulla')) UBERON_0000362 -OBI:0002522 adrenal gland specimen ready for release A specimen that is derived from adrenal gland. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'adrenal gland')) UBERON_0002369 -OBI:0002523 breast specimen ready for release mammary tissue specimen A specimen that is derived from breast. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some breast)) UBERON_0000310 -OBI:0002524 urinary bladder specimen ready for release A specimen that is derived from urinary bladder. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent collecting specimen from organism (tissue and ('part of' some 'urinary bladder')) UBERON_0001255 -OBI:0002525 tibial artery specimen ready for release A specimen that is derived from tibial artery. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 collecting specimen from organism (tissue and ('part of' some vagina)) UBERON_0000996 -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 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 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 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 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 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 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 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 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 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 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 collecting specimen with swab environmental material ENVO_00010483 -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' and ('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 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 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 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 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 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 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 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 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 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 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 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 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 collecting specimen from organism blood UBERON_0000178 -OBI:0003380 placental blood specimen A specimen that is derived from placental blood. VEuPathDB John Judkins equivalent 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 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 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 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 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 lavage -OBI:0003667 oral lavage fluid oral lavage fluid mouth rinse specimen A specimen collected through oral cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the oral cavity space. Sebastian Duesing Anna Maria Masci https://github.com/obi-ontology/obi/issues/1803 equivalent lavage mouth UBERON_0000165 -OBI:0100016 blood plasma specimen blood plasma specimen metadata complete plasma a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended. WEB: http://en.wikipedia.org/wiki/Blood_plasma PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings. PERSON: Maura Gasparetto|PERSON: Melanie Courtot|PERSON: Philippe Rocca-Serra 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA. subclass ('material component separation' and ('has_specified_input' some 'blood specimen')) blood specimen -OBI:0100017 blood serum specimen blood serum specimen metadata complete A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. WEB: http://en.wikipedia.org/wiki/Blood_plasma PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy. PERSON: Maura Gasparetto|PERSON: Melanie Courtot|PERSON: Philippe Rocca-Serra subclass (('filtration' or 'centrifugation' or 'dialysis') and ('has_specified_input' some 'blood specimen')) blood plasma specimen -OBI:0100067 bronchial alveolar lavage bronchial alveolar lavage metadata complete BAL Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space. GROUP: IEDB solution containing lung derived T cells, eosinophils, and TNFa. PERSON: Bjoern Peters equivalent lavage lung -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 ('organ harvesting' and ('has_specified_input' some 'lymph node')) cell specimen -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 ('organ harvesting' and ('has_specified_input' some 'spleen')) cell 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 collecting specimen with swab leukocyte CL_0000738 +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: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: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: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' +OBI:0000950 paraffin specimen paraffin specimen metadata incomplete a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin MO_990 paraffin_sample liver tissue embedded in paraffin PERSON: Chris Stoeckert|PERSON: Jie Zheng equivalent specimen ('paraffin storage' and ('has_specified_input' some ('has role' some 'specimen role'))) +OBI:0000953 processed specimen processed specimen ready for release A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. equivalent specimen 'processed material' and '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: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')) +OBI:0001479 specimen from organism ready for release tissue specimen A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). MO_954 organism_part PERSON: Chris Stoeckert, Jie Zheng equivalent specimen ('organism' or 'material anatomical entity' or 'anatomical cluster') +OBI:0001506 specimen with pre- or post-mortem status specimen with pre- or post-mortem status metadata complete A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. MO_84 OrganismStatus PERSON: Chris Stoeckert, Jie Zheng organizational term, used in description of specimen that is created from known pre- or post-mortem status equivalent specimen ('organism' and ('has quality' some ('alive' or 'dead'))) +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:0002125 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: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: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: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: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 +OBI:0002519 skeletal muscle tissue specimen ready for release A specimen that is derived from skeletal muscle. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism skeletal muscle tissue UBERON_0001134 +OBI:0002520 heart specimen ready for release A specimen that is derived from heart. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some heart)) UBERON_0000948 +OBI:0002521 renal medulla specimen ready for release kidney medulla specimen A specimen that is derived from renal medulla. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'renal medulla')) UBERON_0000362 +OBI:0002522 adrenal gland specimen ready for release A specimen that is derived from adrenal gland. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'adrenal gland')) UBERON_0002369 +OBI:0002523 breast specimen ready for release mammary tissue specimen A specimen that is derived from breast. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some breast)) UBERON_0000310 +OBI:0002524 urinary bladder specimen ready for release A specimen that is derived from urinary bladder. Chris Stoeckert, NCI BBRB Chris Stoeckert equivalent specimen from organism collecting specimen from organism (tissue and ('part of' some 'urinary bladder')) UBERON_0001255 +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: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: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: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 +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: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 +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: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: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 +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: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: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: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: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 +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 +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: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: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 +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: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 +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 +OBI:0003667 oral lavage fluid oral lavage fluid mouth rinse specimen A specimen collected through oral cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the oral cavity space. Sebastian Duesing Anna Maria Masci https://github.com/obi-ontology/obi/issues/1803 equivalent lavage fluid specimen lavage mouth UBERON_0000165 +OBI:0100016 blood plasma specimen blood plasma specimen metadata complete plasma a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended. WEB: http://en.wikipedia.org/wiki/Blood_plasma PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings. PERSON: Maura Gasparetto|PERSON: Melanie Courtot|PERSON: Philippe Rocca-Serra 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA. subclass blood specimen ('material component separation' and ('has_specified_input' some 'blood specimen')) +OBI:0100017 blood serum specimen blood serum specimen metadata complete A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. WEB: http://en.wikipedia.org/wiki/Blood_plasma PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy. PERSON: Maura Gasparetto|PERSON: Melanie Courtot|PERSON: Philippe Rocca-Serra subclass blood plasma specimen (('filtration' or 'centrifugation' or 'dialysis') and ('has_specified_input' some 'blood specimen')) +OBI:0100067 bronchial alveolar lavage bronchial alveolar lavage metadata complete BAL Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space. GROUP: IEDB solution containing lung derived T cells, eosinophils, and TNFa. PERSON: Bjoern Peters equivalent lavage fluid specimen lavage lung +OBI:0302716 pool of specimens pool of specimens metadata complete A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. GROUP: CEBS PERSON: Jennifer Fostel check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish equivalent specimen ('material combination' and ('has_specified_input' only 'specimen')) +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: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 +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: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: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: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