diff --git a/setup.cfg b/setup.cfg index c9f9aac4..1b4c4c03 100644 --- a/setup.cfg +++ b/setup.cfg @@ -151,6 +151,7 @@ ignore = S318 # don't worry about unsafe xml S310 # TODO remove this later and switch to using requests B018 # This is 'useless' statements which are new atm. + B009 # Prevents me from using get_attr after checking has_attr exclude = sssom/sssom_datamodel.py sssom/cliquesummary.py diff --git a/sssom/io.py b/sssom/io.py index 024cb222..9cc97916 100644 --- a/sssom/io.py +++ b/sssom/io.py @@ -28,6 +28,7 @@ from .typehints import Metadata from .util import ( MappingSetDataFrame, + SssomMalformedYamlError, are_params_slots, augment_metadata, is_curie, @@ -114,18 +115,24 @@ def parse_file( def validate_file( - input_path: str, validation_types: List[SchemaValidationType] + input_path: str, validation_types: List[SchemaValidationType], verbose: bool = False ) -> None: """Validate the incoming SSSOM TSV according to the SSSOM specification. :param input_path: The path to the input file in one of the legal formats, eg obographs, aligmentapi-xml :param validation_types: A list of validation types to run. + :param verbose: If true, print detailed error message. """ # Two things to check: # 1. All prefixes in the DataFrame are define in prefix_map # 2. All columns in the DataFrame abide by sssom-schema. - msdf = parse_sssom_table(file_path=input_path) - validate(msdf=msdf, validation_types=validation_types) + try: + msdf = parse_sssom_table(file_path=input_path) + validate(msdf=msdf, validation_types=validation_types) + except SssomMalformedYamlError as e: + print("Your SSSOM mapping set metadata is malformed YAML.") + if verbose: + print(e) def split_file(input_path: str, output_directory: Union[str, Path]) -> None: diff --git a/sssom/parsers.py b/sssom/parsers.py index 1c2ff9f0..1520639a 100644 --- a/sssom/parsers.py +++ b/sssom/parsers.py @@ -58,9 +58,12 @@ URI_SSSOM_MAPPINGS, MappingSetDataFrame, NoCURIEException, + SssomMalformedYamlError, curie_from_uri, get_file_extension, + get_sssom_error_message, is_multivalued_slot, + purl_to_source_id, raise_for_bad_path, read_pandas, to_mapping_set_dataframe, @@ -534,9 +537,13 @@ def from_alignment_minidom( elif node_name == "onto2": ms[OBJECT_SOURCE_ID] = e.firstChild.nodeValue elif node_name == "uri1": - ms[SUBJECT_SOURCE] = e.firstChild.nodeValue + ms[SUBJECT_SOURCE] = purl_to_source_id( + uri=e.firstChild.nodeValue, prefix_map=prefix_map + ) elif node_name == "uri2": - ms[OBJECT_SOURCE] = e.firstChild.nodeValue + ms[OBJECT_SOURCE] = purl_to_source_id( + uri=e.firstChild.nodeValue, prefix_map=prefix_map + ) ms.mappings = mlist # type: ignore _set_metadata_in_mapping_set(mapping_set=ms, metadata=meta) @@ -745,9 +752,12 @@ def _read_metadata_from_table(path: Union[str, Path]) -> Dict[str, Any]: break if yamlstr: - meta = yaml.safe_load(yamlstr) - logging.info(f"Meta={meta}") - return meta + try: + meta = yaml.safe_load(yamlstr) + logging.info(f"Meta={meta}") + return meta + except Exception as e: + raise SssomMalformedYamlError(get_sssom_error_message(e)) return {} diff --git a/sssom/util.py b/sssom/util.py index f56ddfd1..d472a084 100644 --- a/sssom/util.py +++ b/sssom/util.py @@ -941,10 +941,24 @@ def get_dict_from_mapping(map_obj: Union[Any, Dict[Any, Any], SSSOM_Mapping]) -> return map_dict +def get_sssom_error_message(e: Exception): + """Get a human readble error message from an exception.""" + msg = "" + if hasattr(e, "message"): + msg = getattr(e, "message") + else: + str(e) + return msg + + class NoCURIEException(ValueError): """An exception raised when a CURIE can not be parsed with a given prefix map.""" +class SssomMalformedYamlError(ValueError): + """An exception raised when the YAML header is malformed.""" + + CURIE_RE = re.compile(r"[A-Za-z0-9_.]+[:][A-Za-z0-9_]") @@ -1012,6 +1026,19 @@ def get_prefixes_used_in_table(df: pd.DataFrame) -> List[str]: return list(set(prefixes)) +def purl_to_source_id(uri: str, prefix_map: Mapping[str, str]) -> str: + """Parse a CURIE from an PURL to serve as a generic source reference (by splitting of file extension). + + :param uri: The URI to parse. If this is already a CURIE, return directly. + :param prefix_map: The prefix map against which the IRI is checked + :return: A CURIE + """ + curie = curie_from_uri(uri=uri, prefix_map=prefix_map) + if curie.endswith(".owl"): + curie = curie[:-4] + return curie + + def filter_out_prefixes( df: pd.DataFrame, filter_prefixes: List[str], features: list = KEY_FEATURES ) -> pd.DataFrame: @@ -1245,7 +1272,7 @@ def sort_df_rows_columns( col for col in SCHEMA_DICT["slots"].keys() if col in df.columns ] df = df.reindex(column_sequence, axis=1) - if by_rows and len(df) > 0: + if by_rows and len(df) > 0 and len(df.columns) > 0: df = df.sort_values(by=df.columns[0], ignore_index=True) return df diff --git a/sssom/validators.py b/sssom/validators.py index 3e1cf90b..d57cfd82 100644 --- a/sssom/validators.py +++ b/sssom/validators.py @@ -10,18 +10,21 @@ from sssom.context import add_built_in_prefixes_to_prefix_map from sssom.parsers import to_mapping_set_document -from sssom.util import MappingSetDataFrame, get_all_prefixes +from sssom.util import MappingSetDataFrame, SssomMalformedYamlError, get_all_prefixes from .constants import SCHEMA_YAML, SchemaValidationType def validate( - msdf: MappingSetDataFrame, validation_types: List[SchemaValidationType] + msdf: MappingSetDataFrame, + validation_types: List[SchemaValidationType], + verbose=False, ) -> None: """Validate SSSOM files against `sssom-schema` using linkML's validator function. :param msdf: MappingSetDataFrame. :param validation_types: SchemaValidationType + :param verbose: If true, print detailed error message. """ validation_methods = { SchemaValidationType.JsonSchema: validate_json_schema, @@ -29,7 +32,12 @@ def validate( SchemaValidationType.PrefixMapCompleteness: check_all_prefixes_in_curie_map, } for vt in validation_types: - validation_methods[vt](msdf) + try: + validation_methods[vt](msdf) + except SssomMalformedYamlError as e: + print("Your SSSOM mapping set metadata is malformed YAML.") + if verbose: + print(e) def validate_json_schema(msdf: MappingSetDataFrame) -> None: diff --git a/tests/data/hp_mp_kidsfirst_mgi.sssom.tsv b/tests/data/hp_mp_kidsfirst_mgi.sssom.tsv new file mode 100644 index 00000000..1ba15e76 --- /dev/null +++ b/tests/data/hp_mp_kidsfirst_mgi.sssom.tsv @@ -0,0 +1,353 @@ +#mapping_set_id: MGI_KidsFirst_MP_HPO +#mapping_set_title: Mapping of MP terms to HPO terms from KidsFirst list +#mapping_set_description: "HPO terms were provided by the KidsFirst team from the set of terms used for patients in their cohorts. Initially the mapping date was not tracked so these were given the date of when we recieved the file (5/27/21). The set of HPO terms was updated on 5/17/212. Use of skos mappings terms: exact match: MP term is the same as the HPO term, ignoring that the HP term applies only to humans; broad match: MP term covers more than the HPO term; narrow match: MP term is more restircted than the HPO term, ignoring the species restriction; related match: MP term and HPO term share some similarity but would not have a parent-child relation in a shared ontology" +#creator_id: orcid:0000-0003-4606-0597|orcid:0000-0002-6490-7723|ror:021sy4w91|wikidata:Q1951035 +#license: https://creativecommons.org/licenses/by/4.0/ +#mapping_set_group: MGI_MP_HPO +#object_source: http://purl.obolibrary.org/hp.owl +#subject_source: http://purl.obolibrary.org/mp.owl +#curie_map: +# HP: http://purl.obolibrary.org/obo/HP_ +# MP: http://purl.obolibrary.org/obo/MP_ +# skos: http://www.w3.org/2004/02/skos/core/ +# orcid: https://orcid.org/ +# ror: https://ror.org/ +# wikidata: https://www.wikidata.org/wiki/ +subject_id subject_label predicate_id confidence object_id object_label match_type author_id mapping_date comment +hpo_id_phenotype Label Match confidence (0-1) MP ID MP term name HumanCurated orcid comment +HP:0000776 Congenital diaphragmatic hernia skos:broadMatch 0.9 MP:0003924 diaphragmatic hernia HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP does not specify ""congenital"" in the definition" +HP:0011563 Abnormal ventriculoarterial connection skos:broadMatch 0.6 MP:0010426 abnormal heart and great artery attachment HumanCurated orcid:0000-0003-4606-0597 5/27/2021 unclear if all the great arteries are included in the HPO term +HP:0008551 Microtia skos:broadMatch 0.9 MP:0000018 small ears HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "this one just specifies reduced size, can you have reduced size that is not ""underdevelopment""" +HP:0032092 Left ventricular outflow tract obstruction skos:broadMatch 1 MP:0010429 abnormal heart left ventricle outflow tract morphology HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 5/27/2021 "new term, child of abnormal heart left ventricle outflow tract morphology (MP:0010429) we do have stenosis but not obstruction" +HP:0001636 Tetralogy of Fallot skos:broadMatch 1 MP:0002127 abnormal cardiovascular system morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "this is a grouping of multiple phenotypes, may include some but not all of the grouped phenotypes, not inclined to add this to the MP, need to go up to cardiovascular system morphology as the phenotypes include both the heart and blood vessels" +HP:0025031 Abnormality of the digestive system skos:broadMatch 1 MP:0005381 digestive/alimentary phenotype HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "the HPO term covers both morph and physiology, closest match in MP would be the system header but this includes normals" +HP:0000508 Ptosis skos:broadMatch 0.8 MP:0001344 blepharoptosis HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP just specifies ""drooping"" does not include exact measurements as these would differ for different species" +HP:0100659 Abnormality of the cerebral vasculature skos:broadMatch 1 MP:0004950 abnormal brain vasculature morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP does not have a term for cerebral vasculature, whole brain term would be the parent if we added that term, we do have terms for cerebral arteries, add new term for abnormal cerebral vascular morphology, there are a number of annotations to the general brain term that could move" +HP:0004383 Hypoplastic left heart skos:broadMatch 1 MP:0002740 heart hypoplasia HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "child of heart hypoplasia (MP:0002740), 1 existing annotation" +HP:0000238 Hydrocephalus skos:broadMatch 0.7 MP:0001891 hydrocephaly HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "Issue is with the HPO definition that specifies the cause ""resulting from inadequate passage of CSF from its point of production within the cerebral ventricles to its point of absorption"", MP term does not specify a cause. However, both MP and HPO have non-obstructive hydrocephaly/Communicating hydrocephalus as a child term and this type of hydrocephaly does not have an issue with passage. The MP definition for the child term ""abnormal cerebrospinal fluid absorption where there is no obstruction to fluid flow in the ventricular system"" indicating that in this form the absorption is the issue. Based on child terms it is possibly that the hydrocephaly/hydrocephalus terms in MP and HP should be exact." +HP:0001626 Abnormality of the cardiovascular system skos:broadMatch 1 MP:0005385 cardiovascular system phenotype HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP term does not specify ""abnormal"" and is typically used in annotations for mice lacking abnormal phenotypes in the system " +HP:0001762 Talipes equinovarus skos:broadMatch 0.7 MP:0000576 clubfoot HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP definition ""foot is plantarflexed, inverted and adducted"" This is not as specific as the HPO definition. I went with broad as in other species the same criteria may not apply as in the HP definition" +HP:0000077 Abnormality of the kidney skos:broadMatch 1 MP:0005367 renal/urinary system phenotype HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "In this case MP term not only includes ""normals"" but it also includes urinary system phenotypes in addition to kidney phenotypes" +HP:0000118 Phenotypic abnormality skos:broadMatch 1 MP:0000001 mammalian phenotype HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 5/27/2021 the best you could do is the MP root term that covers all phenotypes both normal and abnormal +HP:0000047 Hypospadias skos:broadMatch 1 MP:0003124 hypospadia HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "The MP definition includes abnormal location of urethral opening in both males and females; hpo has just males so this is a broad match, Anna will create subterms for male and female " +HP:0000252 Microcephaly skos:broadMatch 0.8 MP:0000433 microcephaly HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP specifies ""size"" not circumference and does not specify how much smaller" +HP:0002566 Intestinal malrotation skos:broadMatch 0.6 MP:0014023 abnormal intestine placement HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 5/27/2021 "MP:0014023 lacks written definition, the eq uses PATO 'position' which includes orientation so I think the MP term would include the HP phenotypes as well as other placement related phenotypes. We need to add a definition to the MP term" +HP:0000110 Renal dysplasia skos:broadMatch 0.9 MP:0002135 abnormal kidney morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "HPO terms covers both devlopment and morphology, no exact match in MP" +HP:0000110 Renal dysplasia skos:broadMatch 0.9 MP:0000527 abnormal kidney development HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0000369 Low-set ears skos:broadMatch 0.9 MP:0000024 lowered ear position HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "HP term is specific to the location of human ears on the head, MP covers any lowered ear position" +HP:0007970 Congenital ptosis skos:broadMatch 1 MP:0001344 blepharoptosis HumanCurated orcid:0000-0003-4606-0597 5/27/2021 MP term does not specify congenital +HP:0001385 Hip dysplasia skos:broadMatch 0.8 MP:0004509 abnormal pelvic girdle bone morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP is not congenital, based on HPO eq using innominate bone I think this is the correct match" +HP:0000707 Abnormality of the nervous system skos:broadMatch 1 MP:0003631 nervous system phenotype HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0000256 Macrocephaly skos:broadMatch 0.9 MP:0000434 megacephaly HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP term just specifies ""abnormally large size of the head"" not as specific as the HPO term" +HP:0000347 Micrognathia skos:broadMatch 0.9 MP:0002639 micrognathia HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP specifies ""reduced size of the jaws, especially of the mandible"" HPO is specifically mandible hypoplasia, MP term has ""mandibular hypoplasia"" as a narrow synonym" +HP:0001195 Single umbilical artery skos:broadMatch 1 MP:0003230 abnormal umbilical artery morphology HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 5/27/2021 "child of MP:0003230, would need to be modified to make it clear that this was a reduced number of arteries from the normal state. I would assume in some species a single artery might be normal" +HP:0001355 Megalencephaly skos:broadMatch 0.9 MP:0012139 increased forebrain size HumanCurated orcid:0000-0003-4606-0597 5/27/2021 MP covers entire forebrain not just cerebral hemispheres and does not specify consequence +HP:0000113 Polycystic kidney dysplasia skos:broadMatch 0.8 MP:0008528 polycystic kidney HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP term definition does not specify ""both kidneys""" +HP:0004322 Short stature skos:broadMatch 1 MP:0001265 decreased body size HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "includes height, length and weight plus other terms" +HP:0007009 Central nervous system degeneration skos:broadMatch 1 MP:0002229 neurodegeneration HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP has a specific term for peripheral but no term for central, I think Cindy removed most of the peripheral/central terms at one point possibly the peripheral one was missed?" +HP:0002539 Cortical dysplasia skos:broadMatch 1 MP:0000788 abnormal cerebral cortex morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP term does not specificy ""developmental"" cause, also note MP has a separate term for abnormal neocortex morphology, MP term is an exact match to HP:0002538 Abnormal cerebral cortex morphology " +HP:0003302 Spondylolisthesis skos:broadMatch 1 MP:0031313 spondylolisthesis HumanCurated orcid:0000-0002-6490-7723 10/25/2021 "Spondylolisthesis is etymologically directionless and can be applied to both anterolisthesis and retrolisthesis. In clinical practice, spondylolisthesis is used synonymously with anterolisthesis. Often, particularly in the lower lumbar spine, it is due to spondylolysis (pars interarticularis defects). The MP term defintion includes both directions whereas the HPO term definition specifies anterior slippage due to complete bilateral fractures of the pars interarticularis." +HP:0000486 Strabismus skos:broadMatch 1 MP:0005254 strabismus HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP is defined as ""misalignment of the visual axes of the eyes"" without reference to ""bifoveal fixation""" +HP:0000821 Hypothyroidism skos:broadMatch 1 MP:0003503 decreased activity of thyroid gland HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP has hypothyroidism but defines this as ""reduced function of this endocrine gland that normally produces hormones that regulate the metabolic rate of the body"" and has separate terms for abnormal thyroid homone levels. HPO also has terms for thyroid hormone levels but the decreased terms do not relate to hypothyroidism" +HP:0001642 Pulmonic stenosis skos:broadMatch 0.7 MP:0010449 heart right ventricle outflow tract stenosis HumanCurated orcid:0000-0003-4606-0597 8/10/2022 "I think this is exact, note MP has this under morphology while HPO has it under physiology, also the MP eq uses constricted and 'outflow part of right ventricle' while the HPO uses constricted and 'pulmonary valve' but the HPO text definition specifies pulmonary valve and just below the valve so I think the HPO eq is incorrect. MP has a term for pulmonary valve stenosis that uses the pulmonary valve. Also note the HPO term is a child of pulmonary valve physiology so possibly it should be relabeled to be specific to the valve?" +HP:0010960 Bronchopulmonary sequestration skos:broadMatch 0.9 MP:0004880 lung cysts HumanCurated orcid:0000-0003-4606-0597 5/27/2021 not inclined to add a new MP term as I think it is likely to be misused but we can if needed +HP:0000034 Hydrocele testis skos:broadMatch 1 MP:0003623 hydrocele HumanCurated orcid:0000-0002-6490-7723 5/27/2021 "MP term does not specify ""clear"" fluid or where accumulation occurs (space between the layers of the tunica vaginalis)" +HP:0001511 Intrauterine growth retardation skos:broadMatch 1 MP:0010865 prenatal growth retardation HumanCurated orcid:0000-0003-4606-0597 8/10/2022 "MP does not specify the percentile but would cover the meaning of the HP term, MP also covers embryonic and fetal stages" +HP:0002032 Esophageal atresia skos:broadMatch 0.9 MP:0003276 esophageal atresia HumanCurated orcid:0000-0003-4606-0597 7/15/2021 "MP definition specifies ""congenital blockage or absence"" while HP specifies ""complete obliteration of the lumen of the esophagus"" I would not consider blockage to =obliteration of the lumen but absence would = obliteration so I consider the MP term to be broader than the HP term " +HP:0005815 Supernumerary ribs skos:broadMatch 1 MP:0000480 increased number of ribs HumanCurated orcid:0000-0003-4606-0597 7/15/2021 "MP specifies greater than normal number while HPO specifies what the normal number is for humans, conceptually these are the same but MP is broader to cover species with a different ""normal"" rib number" +HP:0007033 Cerebellar dysplasia skos:broadMatch 1 MP:0000849 abnormal cerebellum morphology HumanCurated orcid:0000-0003-4606-0597 7/15/2021 "While the morphology term has ""dysplasia"" as an exact synonym not all of the phenotypes under this term relate to ""growth or development"" thus it is broader than the HPO term. Conversely the developmnet term is I think narrower as some phenotypes seen in adults that are the end product of developmental issues will only appear under morphology" +HP:0012583 Unilateral renal hypoplasia skos:broadMatch 1 MP:0003446 renal hypoplasia HumanCurated orcid:0000-0003-4606-0597 9/30/2021 "MP term cover unilateral and bilateral, consider splitting, there are annotations that could be moved to the new term" +HP:0000081 Duplicated collecting system skos:broadMatch 0.6 MP:0011803 double kidney pelvis HumanCurated orcid:0000-0003-4606-0597 9/30/2021 "The MP does not have a term for renal collecting system but looking at the HPO definition of duplicated collecting system, in particulatr ""kidney with two (instead of, normally, one) pyelocaliceal systems. The pyelocaliceal system is comprised of the renal pelvis and calices."" and the Uberon and MP organization of renal pelvis and renal calyx (calyx is part of pelvis), it seemed to me that the MP double pelvis term is as close as I could get. There may be some distinction I'm missing as the HPO has a term for ""Duplication of renal pelvis"" (HP:0005580) but it is unclear to me how this is distinct from duplicated collecting system. I'm guessing that the pelvis includes parts that are not part of the collecting system? Uberon has a term for renal collecting system (UBERON:0004100) defined as collecting duct system of the kidney consists of a series of tubules and ducts that connect the nephrons to the ureter and this has no connection to the renal pelvis and calyx. Given that the duplicated HP term specifies pelvis and calices I would have expected some connection. " +HP:0000085 Horseshoe kidney skos:broadMatch 1 MP:0003605 fused kidneys HumanCurated orcid:0000-0002-6490-7723 9/20/2021 "HPO term for Horseshoe kidney HP:0000085 uses ""Fused kidneys"" as a broad synonym. Conversely, MP term for fused kidneys MP:0003605 uses ""horseshoe kidney"" as a narrow synonym " +HP:0001161 Hand polydactyly skos:broadMatch 1 MP:0000562 polydactyly HumanCurated orcid:0000-0003-4606-0597 1/25/2022 create new children for fore and hindlimb polydactyly +HP:0001840 Metatarsus adductus skos:broadMatch 1 MP:0003072 abnormal metatarsal bone morphology HumanCurated orcid:0000-0003-4606-0597 1/25/2022 "consider adding new child, at least a general rotation term" +HP:0010492 Osseous finger syndactyly skos:broadMatch 0.8 MP:0008730 fused phalanges HumanCurated orcid:0000-0003-4606-0597 1/25/2022 MP term is not limited to fingers but given defintions and placement I think MP term is better mapped as broad rather than related +HP:0030043 Hip subluxation skos:broadMatch 1 MP:0030829 abnormal hip joint morphology HumanCurated orcid:0000-0003-4606-0597 1/25/2022 "consider adding new term, no existing annotations in MGI" +HP:0002616 Aortic root aneurysm skos:broadMatch 1 MP:0011575 dilated aorta bulb HumanCurated orcid:0000-0003-4606-0597 1/25/2022 "MP term does not include ""localized"" in the definition, there are MGI annotations that specify aneurysm, so add new term" +HP:0010945 Fetal pyelectasis skos:broadMatch 1 MP:0000519 hydronephrosis HumanCurated orcid:0000-0003-4606-0597 1/26/2022 +HP:0045005 Neural tube defect skos:broadMatch 1 MP:0003720 abnormal neural tube closure HumanCurated orcid:0000-0003-4606-0597 1/26/2022 "note ""neural tube defects"" is a synonym of abnormal neural tube morphology in the MP but the HPO term specfies a defect in closure; the MP term specifies ""any anomaly"" in closure and could thus cover premature closure while the HPO term specifies ""fails to close"". In practice the child terms of the MP term all relate to failure or delay of closure" +HP:0100333 Unilateral cleft lip skos:broadMatch 1 MP:0005170 cleft upper lip HumanCurated orcid:0000-0003-4606-0597 1/26/2022 +HP:0000054 Micropenis skos:broadMatch 1 MP:0005188 small penis HumanCurated orcid:0000-0002-6490-7723 5/27/2021 "MP definition just refers to ""reduced size"", does not specify penis length but uses microphallus and micropenis as exact synonyms. Also, EQ for HPO term uses hypoplastic rather than decreased size" +HP:0000079 Abnormality of the urinary system skos:broadMatch 1 MP:0005367 renal/urinary system phenotype HumanCurated orcid:0000-0003-4606-0597 1/26/2022 "Direct annotations to this term are for ""normal"" annotations but all children are abnormal " +HP:0000158 Macroglossia skos:broadMatch 1 MP:0009906 increased tongue size HumanCurated orcid:0000-0002-6490-7723 5/27/2021 "MP definition does not specify ""increased length and width""" +HP:0000185 Cleft soft palate skos:broadMatch 0.9 MP:0013546 cleft soft palate HumanCurated orcid:0000-0002-6490-7723 5/27/2021 MP definition does not specify time window of developmental defect or its functional consequences +HP:0001776 Bilateral talipes equinovarus skos:broadMatch 1 MP:0000576 clubfoot HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0001829 Foot polydactyly skos:broadMatch 1 MP:0000562 polydactyly HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0003316 Butterfly vertebrae skos:broadMatch 1 MP:0000141 abnormal vertebral body morphology HumanCurated orcid:0000-0002-6490-7723 12/20/2021 "consider adding a term for vertebral body cleft, there are a number of existing annotations for split vertebrae" +HP:0025247 Dermoid cyst skos:broadMatch 1 MP:0031309 skin cyst HumanCurated orcid:0000-0003-4606-0597 1/27/2022 existing annotation J:186934 +HP:0100711 Abnormal thoracic spine morphology skos:broadMatch 1 MP:0004703 abnormal vertebral column morphology HumanCurated orcid:0000-0003-4606-0597 1/27/2022 many annotations specify thoracic spinal column ticket https://github.com/mgijax/mammalian-phenotype-ontology/issues/3498 +HP:0000133 Gonadal dysgenesis skos:broadMatch 0.8 MP:0002211 abnormal primary sex determination HumanCurated orcid:0000-0003-4606-0597 1/27/2022 "uncertainty due to absence of definition for HPO term, based on definition of child terms and placement in the hierarchy I think the MP term is broader than the HPO term" +HP:0000218 High palate skos:broadMatch 1 MP:0003757 high palate HumanCurated orcid:0000-0003-4606-0597 1/27/2022 broad as the MP term does not have the 2SD above the mean restriction +HP:0000824 Decreased response to growth hormone stimulation test skos:broadMatch 1 MP:0005120 decreased circulating growth hormone level HumanCurated orcid:0000-0003-4606-0597 1/27/2022 "going with broad since the HPO term has ""responses to growth hormone (GH) provocation tests"" in the definition while the MP term covers lower levels regardless of the test" +HP:0000957 Cafe-au-lait spot skos:broadMatch 1 MP:0002095 abnormal skin pigmentation HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0001290 Generalized hypotonia skos:broadMatch 1 MP:0004144 hypotonia HumanCurated orcid:0000-0003-4606-0597 1/27/2022 "MP broad based on lack of ""generalized"" specification" +HP:0001601 Laryngomalacia skos:broadMatch 1 MP:0002249 abnormal larynx morphology HumanCurated orcid:0000-0003-4606-0597 1/27/2022 no related annotations in MGI +HP:0001682 Subvalvular aortic stenosis skos:broadMatch 1 MP:0010463 aorta stenosis HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0002059 Cerebral atrophy skos:broadMatch 1 MP:0012508 forebrain atrophy HumanCurated orcid:0000-0003-4606-0597 1/28/2022 +HP:0004209 Clinodactyly of the 5th finger skos:broadMatch 1 MP:0006253 clinodactyly HumanCurated orcid:0000-0003-4606-0597 1/28/2022 +HP:0004969 Peripheral pulmonary artery stenosis skos:broadMatch 1 MP:0010457 pulmonary artery stenosis HumanCurated orcid:0000-0003-4606-0597 1/28/2022 +HP:0004970 Ascending tubular aorta aneurysm skos:broadMatch 1 MP:0010483 ascending aorta aneurysm HumanCurated orcid:0000-0003-4606-0597 1/28/2022 +HP:0005301 Persistent left superior vena cava skos:broadMatch 1 MP:0006064 abnormal superior vena cava morphology HumanCurated orcid:0000-0003-4606-0597 1/28/2022 "MP has a term for ""abnormal left vena cava superior connection"" but this lacks a definition so it is unclear how it relates to the HPO term. Ticket https://github.com/mgijax/mammalian-phenotype-ontology/issues/3501 " +HP:0008780 Congenital bilateral hip dislocation skos:broadMatch 1 MP:0030796 hip dislocation HumanCurated orcid:0000-0003-4606-0597 1/31/2022 +HP:0010305 Absence of the sacrum skos:broadMatch 1 MP:0010113 abnormal sacrum morphology HumanCurated orcid:0000-0003-4606-0597 1/31/2022 "As the sacrum is formed by fusion of the sacral vertebrae in humans and tailles primates would it be better to map to absent sacral vertebrae, " +HP:0010880 Increased nuchal translucency skos:broadMatch 1 MP:0012723 abnormal nuchal region morphology HumanCurated orcid:0000-0003-4606-0597 2/2/2022 +HP:0010959 Congenital cystic adenomatoid malformation of the lung skos:broadMatch 1 MP:0004880 lung cyst HumanCurated orcid:0000-0003-4606-0597 2/2/2022 +HP:0012516 Tetralogy of Fallot with pulmonary atresia skos:broadMatch 1 MP:0002127 abnormal cardiovascular system morphology HumanCurated orcid:0000-0003-4606-0597 2/2/2022 +HP:0025480 Lipomyelomeningocele skos:broadMatch 1 MP:0009929 meningomyelocele HumanCurated orcid:0000-0003-4606-0597 2/2/2022 +HP:0030708 Myeloschisis skos:broadMatch 1 MP:0009929 meningomyelocele HumanCurated orcid:0000-0003-4606-0597 2/2/2022 +HP:0030799 Scaphocephaly skos:broadMatch 1 MP:0003742 narrow head HumanCurated orcid:0000-0003-4606-0597 2/2/2022 +HP:0100336 Bilateral cleft lip skos:broadMatch 1 MP:0005170 cleft upper lip HumanCurated orcid:0000-0003-4606-0597 2/2/2022 +HP:0100802 Malposition of the stomach skos:broadMatch 0.9 MP:0010807 abnormal stomach position or orientation HumanCurated orcid:0000-0003-4606-0597 2/2/2022 "MP term covers position and rotation but HP term is only position, some uncertainty if the intent was for malrotation to have a separate term" +HP:0200151 Cutaneous mastocytosis skos:broadMatch 1 MP:0000324 increased mast cell number HumanCurated orcid:0000-0003-4606-0597 2/7/2022 https://github.com/mgijax/mammalian-phenotype-ontology/issues/3510 +HP:0000033 "Ambiguous genitalia, male" skos:broadMatch 1 MP:0009198 abnormal male genitalia morphology HumanCurated orcid:0000-0003-4606-0597 2/7/2022 "existing annotations from J:15425, J:98554 annotations are scattered under various terms, https://github.com/mgijax/mammalian-phenotype-ontology/issues/3511" +HP:0000049 Shawl scrotum skos:broadMatch 1 MP:0002669 abnormal scrotum morphology HumanCurated orcid:0000-0003-4606-0597 2/11/2022 no relevant annotations in MGI +HP:0000075 Renal duplication skos:broadMatch 0.8 MP:0004017 duplex kidney HumanCurated orcid:0000-0003-4606-0597 2/11/2022 "MP term specifies that the kidney is split but there may or may not be duplication of the ureter, HPO definition specifies duplication of the kidney, renal pelvis and ureter. However, partial duplication of the kidney is a child of renal duplication so possibly the definition is overly restrictive?" +HP:0000341 Narrow forehead skos:broadMatch 1 MP:0030045 abnormal forehead shape HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 2/11/2022 no annotations in MGI for narrow +HP:0000378 Cupped ear skos:broadMatch 0.9 MP:0003735 cup-shaped ears HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 2/11/2022 "definitions are very different but I am reasonably confident that the HP term would within the range of the MP term, uncertainty mainly about wether this could be an exact or close match" +HP:0000396 Overfolded helix skos:broadMatch 1 MP:0030092 abnormal outer ear helix morphology HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 2/11/2022 +HP:0000465 Webbed neck skos:broadMatch 0.9 MP:0012077 webbed neck HumanCurated orcid:0000-0003-4606-0597 6/21/2022 +HP:0000476 Cystic hygroma skos:broadMatch 1 MP:0031310 abnormal cyst HumanCurated orcid:0000-0003-4606-0597 6/21/2022 +HP:0000582 Upslanted palpebral fissure skos:broadMatch 1 MP:0001340 abnormal eyelid morphology HumanCurated orcid:0000-0003-4606-0597 6/21/2022 +HP:0000588 Optic nerve coloboma skos:broadMatch 0.9 MP:0010717 optic nerve coloboma HumanCurated orcid:0000-0003-4606-0597 6/21/2022 "MP term does not specify ""extends inferiorly"" " +HP:0000627 Posterior embryotoxon skos:broadMatch 1 MP:0006250 abnormal line of Schwalbe morphology HumanCurated orcid:0000-0003-4606-0597 6/21/2022 +HP:0000639 Nystagmus skos:broadMatch 0.9 MP:0004844 abnormal vestibuloocular reflex HumanCurated orcid:0000-0003-4606-0597 6/21/2022 The MP term covers any abnormality in this reflex +HP:0000646 Amblyopia skos:broadMatch 1 MP:0006149 decreased visual acuity HumanCurated orcid:0000-0003-4606-0597 6/21/2022 +HP:0000823 Delayed puberty skos:broadMatch 0.9 MP:0001938 delayed sexual maturation HumanCurated orcid:0000-0003-4606-0597 8/12/2022 +HP:0001780 Abnormality of toe skos:broadMatch 1 MP:0002110 abnormal digit morphology HumanCurated orcid:0000-0002-6490-7723 8/10/2022 "HPO term is a child term of ""abnormal digit morphology"". MP term uses abnormal toe morphology as a narrow synonym. " +HP:0000322 Short philtrum skos:broadMatch 0.9 MP:0030193 short philtrum HumanCurated orcid:0000-0002-6490-7723 9/20/2021 "MP term definition does not include exact measurements and does not use ""vertical hypoplasia of philtrum"" as an exact synonym so I consider the MP term to be borader than the HPO term" +HP:0000411 Protruding ear skos:broadMatch 1 MP:0000021 prominent ears HumanCurated orcid:0000-0002-6490-7723 9/20/2021 MP does not specifiy exact measurements so I consider this broader than the HPO term +HP:0001734 Annular pancreas skos:broadMatch 1 MP:0006261 annular pancreas HumanCurated orcid:0000-0002-6490-7723 5/27/2021 "MP term definition does not specify additional detail such as ""congenital"", ""complete or incomplete"" enciclement of the ""second portion of duodenum"" or occasional ""obstruction"" of the more proximal part" +HP:0003304 Spondylolysis skos:broadMatch 1 MP:0031312 spondylolysis HumanCurated orcid:0000-0002-6490-7723 10/25/2021 "MP term doe not specify ""developmental or acquired"" stress fracture and ""secondary to chronic low-grade trauma""" +HP:0011570 Congenital mitral stenosis skos:broadMatch 1 MP:0006122 mitral valve stenosis HumanCurated orcid:0000-0002-6490-7723 12/20/2021 MP term does not specify congenital onset and is thus an exact match to HPO term Mitral stenosis HP:0005163 rather than Congenital mitral stenosis HP:0011570 +HP:0031805 Intraretinal hemorrhage skos:broadMatch 1 MP:0006185 retinal hemorrhage HumanCurated orcid:0000-0002-6490-7723 12/20/2021 MP term is just defined as bleeding into the retina +HP:0200012 Short corpus callosum skos:broadMatch 1 MP:0000781 decreased corpus callosum size HumanCurated orcid:0000-0002-6490-7723 12/20/2021 HPO provides no textutal definition +HP:0001374 Congenital hip dislocation skos:closeMatch 0.7 MP:0030796 hip dislocation HumanCurated orcid:0000-0003-4606-0597 5/27/2021 no mention of congenital in MP term +HP:0000316 Hypertelorism skos:closeMatch 0.9 MP:0001300 ocular hypertelorism HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP term does not include the ""2 SD"" requirement but would be an exact match to the ""alternate"" definition" +HP:0000041 Chordee skos:closeMatch 0.7 MP:0003555 chordee HumanCurated orcid:0000-0002-6490-7723 9/20/2021 "The MP term definition for chordee MP:0003555 specifies ""acute angulation of the penis upon erection"" and places chordee under abnormal penile erection MP:0001379, unlike HPO which places Chordee HP:0000041 under Abnormal penis morphology HP:0000036 and provides details on the direction of bowing and degree of angulation. I think the match is therefore ""close"" and the MP term should be placed under both abnormal penile erection and morphology (see https://educalingo.com/en/dic-en/chordee)" +HP:0004942 Aortic aneurysm skos:closeMatch 0.9 MP:0006278 aortic aneurysm HumanCurated orcid:0000-0003-4606-0597 1/25/2022 "slight uncertainty based on specificity of HPO definition relative to MP definition, usage may not always be exact so I went with close" +HP:0000175 Cleft palate skos:exactMatch 1 MP:0000111 cleft palate HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0010438 Abnormal ventricular septum morphology skos:exactMatch 1 MP:0000281 abnormal interventricular septum morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001641 Abnormal pulmonary valve morphology skos:exactMatch 1 MP:0002748 abnormal pulmonary valve morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0011994 Abnormal atrial septum morphology skos:exactMatch 1 MP:0000282 abnormal interatrial septum morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001679 Abnormal aortic morphology skos:exactMatch 1 MP:0000272 abnormal aorta morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 add HPO as synonym +HP:0008551 Microtia skos:exactMatch 1 MP:0030297 outer ear hypoplasia HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001707 Abnormal right ventricle morphology skos:exactMatch 1 MP:0003920 abnormal heart right ventricle morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001646 Abnormal aortic valve morphology skos:exactMatch 1 MP:0002747 abnormal aortic valve morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001633 Abnormal mitral valve morphology skos:exactMatch 1 MP:0000286 abnormal mitral valve morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001627 Abnormal heart morphology skos:exactMatch 1 MP:0000266 abnormal heart morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001711 Abnormal left ventricle morphology skos:exactMatch 1 MP:0003921 abnormal heart left ventricle morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0040106 Morphological abnormality of the lateral semicircular canal skos:exactMatch 1 MP:0000037 abnormal lateral semicircular canal morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0007628 Mandibular condyle hypoplasia skos:exactMatch 1 MP:0030259 mandibular condyloid process hypoplasia HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0030966 Abnormal pulmonary artery morphology skos:exactMatch 1 MP:0000484 abnormal pulmonary artery morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001702 Abnormal tricuspid valve morphology skos:exactMatch 1 MP:0002624 abnormal tricuspid valve morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0011546 Abnormal atrioventricular connection skos:exactMatch 1 MP:0010435 abnormal heart atrium and ventricle connection HumanCurated orcid:0000-0003-4606-0597 5/27/2021 add synonym +HP:0002624 Abnormal venous morphology skos:exactMatch 1 MP:0002725 abnormal vein morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 add synonym +HP:0030319 Weakness of facial musculature skos:exactMatch 1 MP:0031314 facial muscle weakness HumanCurated orcid:0000-0002-6490-7723 10/25/2021 new term - child of muscle weakness (MP:0000747) I do not see any existing annotations mentioning face or facial under this term +HP:0000324 Facial asymmetry skos:exactMatch 1 MP:0030099 facial asymmetry HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0002650 Scoliosis skos:exactMatch 1 MP:0000161 scoliosis HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0030853 Heterotaxy skos:exactMatch 1 MP:0004133 heterotaxia HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001631 Atrial septal defect skos:exactMatch 1 MP:0010403 atrial septal defect HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001252 Muscular hypotonia skos:exactMatch 0.9 MP:0004144 hypotonia HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "based on definitions these are the same, but note that the MP definition states that hypotonia shoud not be confused with weakness while the HP includes ""Low or weak muscle tone"" as a synonym. I think this is fine since it specifies ""tone"" but I knocked the confidence down to 9 because of this - smb" +HP:0000708 Behavioral abnormality skos:exactMatch 1 MP:0004924 abnormal behavior HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0005344 Abnormal carotid artery morphology skos:exactMatch 1 MP:0004181 abnormal carotid artery morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0100545 Arterial stenosis skos:exactMatch 1 MP:0006135 artery stenosis HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0030968 Abnormal pulmonary vein morphology skos:exactMatch 1 MP:0002726 abnormal pulmonary vein morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0000384 Preauricular skin tag skos:exactMatch 1 MP:0031305 preauricular skin tag HumanCurated orcid:0000-0002-6490-7723 10/12/2021 child of abnormal periauricular region morphology (MP:0030096) +HP:0006704 Abnormal coronary artery morphology skos:exactMatch 1 MP:0004111 abnormal coronary artery morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0000122 Unilateral renal agenesis skos:exactMatch 1 MP:0003604 single kidney HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0000364 Hearing abnormality skos:exactMatch 0.8 MP:0001963 abnormal hearing physiology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP definition is ""any functional anomaly in the ability to perceive auditory stimuli"" I think this is an exact match to the HPO term" +HP:0001643 Patent ductus arteriosus skos:exactMatch 1 MP:0003139 patent ductus arteriosus HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0000929 Abnormal skull morphology skos:exactMatch 0.9 MP:0000438 abnormal cranium morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP definition is ""any structural anomaly of the bones of the head"", only question would be are there any bones of the head that would not be considered part of the skull. I think the intended meaning is the same as that of the HP term" +HP:0001999 Abnormal facial shape skos:exactMatch 1 MP:0030071 abnormal face shape HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0011821 Abnormality of facial skeleton skos:exactMatch 1 MP:0005274 abnormal viscerocranium morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0000028 Cryptorchidism skos:exactMatch 1 MP:0002286 cryptorchism HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0002414 Spina bifida skos:exactMatch 1 MP:0003054 spina bifida HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001655 Patent foramen ovale skos:exactMatch 1 MP:0004225 patent cardiac foramen ovale HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001684 Secundum atrial septal defect skos:exactMatch 1 MP:0010405 ostium secundum atrial septal defect HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0010296 Ankyloglossia skos:exactMatch 1 MP:0013264 tongue ankylosis HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001629 Ventricular septal defect skos:exactMatch 1 MP:0010402 ventricular septal defect HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0004307 Abnormal anatomic location of the heart skos:exactMatch 0.8 MP:0006065 abnormal heart position or orientation HumanCurated orcid:0000-0003-4606-0597 5/27/2021 HPO defintion does not mention orientation but child terms include orientation specific ones so I'm assuming these are exact +HP:0001746 Asplenia skos:exactMatch 1 MP:0000690 absent spleen HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0002475 Myelomeningocele skos:exactMatch 1 MP:0009929 meningomyelocele HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0011620 Abnormality of abdominal situs skos:exactMatch 1 MP:0031284 abdominal situs abnormality HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 5/27/2021 MP has MP:0011250 and MP:0011249 but not the parent grouping term +HP:0025580 Abnormal right atrium morphology skos:exactMatch 1 MP:0003922 abnormal heart right atrium morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0000767 Pectus excavatum skos:exactMatch 1 MP:0012514 pectus excavatum HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 5/27/2021 +HP:0000568 Microphthalmia skos:exactMatch 0.8 MP:0001297 microphthalmia HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP definition uses plural ""eyes"" but I think these are exact match and I would not be surprised to find annotations of models with unilateral microphthalmia annotated to the MP term, we may want to clarify the definition" +HP:0025579 Abnormal left atrium morphology skos:exactMatch 1 MP:0003923 abnormal heart left atrium morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0000174 Abnormal palate morphology skos:exactMatch 1 MP:0003755 abnormal palate morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0012638 Abnormal nervous system physiology skos:exactMatch 1 MP:0003633 abnormal nervous system physiology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0002408 Cerebral arteriovenous malformation skos:exactMatch 1 MP:0010530 cerebral arteriovenous malformation HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0000074 Ureteropelvic junction obstruction skos:exactMatch 1 MP:0011491 ureteropelvic junction obstruction HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001680 Coarctation of aorta skos:exactMatch 1 MP:0003387 aorta coarctation HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0002089 Pulmonary hypoplasia skos:exactMatch 1 MP:0001178 pulmonary hypoplasia HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0012443 Abnormality of brain morphology skos:exactMatch 1 MP:0002152 abnormal brain morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0000365 Hearing impairment skos:exactMatch 1 MP:0006325 impaired hearing HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001363 Craniosynostosis skos:exactMatch 1 MP:0000081 premature cranial suture closure HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0002575 Tracheoesophageal fistula skos:exactMatch 1 MP:0003321 tracheoesophageal fistula HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0006707 Abnormality of the hepatic vasculature skos:exactMatch 1 MP:0009820 abnormal liver vasculature morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0000107 Renal cyst skos:exactMatch 0.9 MP:0003675 kidney cysts HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "while the HP term is singular and the MP plural, the HP term has multiple cysts as a child term and the MP term does not specify that it has to be multiple, so I think these are an exact match" +HP:0000682 Abnormality of dental enamel skos:exactMatch 1 MP:0002576 abnormal enamel morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0002023 Anal atresia skos:exactMatch 1 MP:0003130 anal atresia HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0410042 Abnormal liver morphology skos:exactMatch 1 MP:0000598 abnormal liver morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001647 Bicuspid aortic valve skos:exactMatch 1 MP:0010484 bicuspid aortic valve HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0010309 Bifid sternum skos:exactMatch 1 MP:0004320 split sternum HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0012741 Unilateral cryptorchidism skos:exactMatch 1 MP:0031286 unilateral cryptorchism HumanCurated orcid:0000-0002-6490-7723 7/26/2021 +HP:0000126 Hydronephrosis skos:exactMatch 1 MP:0000519 hydronephrosis HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001320 Cerebellar vermis hypoplasia skos:exactMatch 1 MP:0000866 cerebellum vermis hypoplasia HumanCurated orcid:0000-0002-6490-7723 5/27/2021 +HP:0000925 Abnormality of the vertebral column skos:exactMatch 1 MP:0004703 abnormal vertebral column morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001321 Cerebellar hypoplasia skos:exactMatch 1 MP:0000851 cerebellum hypoplasia HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001659 Aortic regurgitation skos:exactMatch 1 MP:0006047 aortic valve regurgitation HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0002786 Tracheobronchomalacia skos:exactMatch 1 MP:0031308 tracheobronchomalacia HumanCurated orcid:0000-0003-4606-0597 8/10/2022 "MP term does not provide functional consequences but given that this is a ""may have"" I think we can ignore the difference" +HP:0002948 Vertebral fusion skos:exactMatch 1 MP:0004609 vertebral fusion HumanCurated orcid:0000-0003-4606-0597 8/10/2022 +HP:0031411 Abnormal chromosome morphology skos:exactMatch 1 MP:0003702 abnormal chromosome morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0002021 Pyloric stenosis skos:exactMatch 1 MP:0003307 pyloric stenosis HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0012020 Right aortic arch skos:exactMatch 1 MP:0004158 right aortic arch HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0031703 Abnormal ear morphology skos:exactMatch 1 MP:0002102 abnormal ear morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001539 Omphalocele skos:exactMatch 1 MP:0003052 omphalocele HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0000023 Inguinal hernia skos:exactMatch 1 MP:0006077 inguinal hernia HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0000070 Ureterocele skos:exactMatch 0.9 MP:0011767 ureterocele HumanCurated orcid:0000-0003-4606-0597 8/10/2022 "each definition has details that may or may not be essential to the differentia of the phenotype, checked Tabers and other sources and I think these are defining the same thing" +HP:0001250 Seizure skos:exactMatch 0.8 MP:0002064 seizures HumanCurated orcid:0000-0003-4606-0597 8/10/2022 each definition has details that are distinct but I think the intention is to describe the same phenotype +HP:0001653 Mitral regurgitation skos:exactMatch 1 MP:0006045 mitral valve regurgitation HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001719 Double outlet right ventricle skos:exactMatch 1 MP:0000284 double outlet right ventricle HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0008081 Pes valgus skos:exactMatch 1 MP:0031291 pes valgus HumanCurated orcid:0000-0002-6490-7723 9/20/2021 "new term, parent would be abnormal autopod morphology, need to consider if this would be hindlimb autopod specific" +HP:0010775 Vascular ring skos:exactMatch 1 MP:0010466 vascular ring HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 7/15/2021 +HP:0011480 Unilateral microphthalmos skos:exactMatch 1 MP:0031289 unilateral microphthalmia HumanCurated orcid:0000-0002-6490-7723 9/20/2021 "new term, parent would be MP:0001297" +HP:0000358 Posteriorly rotated ears skos:exactMatch 1 MP:0003715 posteriorly rotated ears HumanCurated orcid:0000-0003-4606-0597 1/25/2022 +HP:0000413 Atresia of the external auditory canal skos:exactMatch 1 MP:0009707 absent external auditory canal HumanCurated orcid:0000-0003-4606-0597 1/25/2022 +HP:0002084 Encephalocele skos:exactMatch 1 MP:0012260 encephalomeningocele HumanCurated orcid:0000-0003-4606-0597 1/25/2022 +HP:0002247 Duodenal atresia skos:exactMatch 1 MP:0003272 duodenal atresia HumanCurated orcid:0000-0003-4606-0597 1/25/2022 +HP:0002937 Hemivertebrae skos:exactMatch 0.9 MP:0008832 hemivertebra HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 8/10/2022 "MP definition specifies ""congenital malformation of the spine"" in which only half of a vertebral body develops, checking the comment and cross-references on the HPO term I (smb) think these are exact" +HP:0004415 Pulmonary artery stenosis skos:exactMatch 1 MP:0010457 pulmonary artery stenosis HumanCurated orcid:0000-0002-6490-7723 1/25/2022 "MP definition does not specify ""main pulmonary artery and/or left or right pulmonary artery branches""" +HP:0010445 Primum atrial septal defect skos:exactMatch 1 MP:0010404 ostium primum atrial septal defect HumanCurated orcid:0000-0003-4606-0597 1/25/2022 +HP:0011623 Muscular ventricular septal defect skos:exactMatch 1 MP:0010420 muscular ventricular septal defect HumanCurated orcid:0000-0003-4606-0597 1/25/2022 +HP:0000089 Renal hypoplasia skos:exactMatch 1 MP:0003446 renal hypoplasia HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 1/25/2022 +HP:0000405 Conductive hearing impairment skos:exactMatch 1 MP:0006326 conductive hearing impairment HumanCurated orcid:0000-0003-4606-0597 1/25/2022 +HP:0001651 Dextrocardia skos:exactMatch 1 MP:0000644 dextrocardia HumanCurated orcid:0000-0003-4606-0597 1/25/2022 +HP:0002836 Bladder exstrophy skos:exactMatch 1 MP:0013282 urinary bladder exstrophy HumanCurated orcid:0000-0002-6490-7723 12/20/2021 +HP:0000407 Sensorineural hearing impairment skos:exactMatch 1 MP:0006329 sensorineural hearing impairment HumanCurated orcid:0000-0003-4606-0597 1/26/2022 +HP:0000470 Short neck skos:exactMatch 1 MP:0012721 short neck HumanCurated orcid:0000-0002-6490-7723 5/27/2021 +HP:0000473 Torticollis skos:exactMatch 1 MP:0030126 torticollis HumanCurated orcid:0000-0002-6490-7723 5/27/2021 +HP:0000609 Optic nerve hypoplasia skos:exactMatch 1 MP:0006221 optic nerve hypoplasia HumanCurated orcid:0000-0002-6490-7723 5/27/2021 +HP:0000766 Abnormal sternum morphology skos:exactMatch 1 MP:0000157 abnormal sternum morphology HumanCurated orcid:0000-0003-4606-0597 1/26/2022 +HP:0001000 Abnormality of skin pigmentation skos:exactMatch 1 MP:0002095 abnormal skin pigmentation HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 1/26/2022 "MP textual definition includes ""changes in the amount, shape, or distribution of cells producing pigment"". The HPO term is synonymous to abnormal skin color. Note that there is an existing MP parent term for abnormal skin coloration MP:0011239 - smb: I think the skin color synonyms ought to be broad since skin color can change based on non-pigment related reasons. Based on definitions and placement I think these are an exact match " +HP:0001159 Syndactyly skos:exactMatch 1 MP:0000564 syndactyly HumanCurated orcid:0000-0003-4606-0597 1/26/2022 +HP:0001750 Single ventricle skos:exactMatch 1 MP:0010432 common ventricle HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0003244 Penile hypospadias skos:exactMatch 1 MP:0031294 penile hypospadia HumanCurated orcid:0000-0002-6490-7723 12/20/2021 +HP:0010735 Polyostotic fibrous dysplasia skos:exactMatch 1 MP:0031350 polyostotic fibrous dysplasia HumanCurated orcid:0000-0003-4606-0597|orcid:0000-0002-6490-7723 2/1/2022 see ticket https://github.com/mgijax/mammalian-phenotype-ontology/issues/3497 +HP:0011590 Double aortic arch skos:exactMatch 1 MP:0004159 double aortic arch HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0012303 Abnormal aortic arch morphology skos:exactMatch 1 MP:0004113 abnormal aortic arch morphology HumanCurated orcid:0000-0002-6490-7723 12/20/2021 MP term refers specifically to the adult aortic arch structure and includes details on branches +HP:0000359 Abnormality of the inner ear skos:exactMatch 1 MP:0000026 abnormal inner ear morphology HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0000372 Abnormality of the auditory canal skos:exactMatch 1 MP:0006033 abnormal external auditory canal morphology HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0000519 Developmental cataract skos:exactMatch 1 MP:0031345 developmental cataract HumanCurated orcid:0000-0003-4606-0597|orcid:0000-0002-6490-7723 2/1/2022 ticket https://github.com/mgijax/mammalian-phenotype-ontology/issues/3499 +HP:0000565 Esotropia skos:exactMatch 1 MP:0005256 esotropia HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0000587 Abnormality of the optic nerve skos:exactMatch 1 MP:0001330 abnormal optic nerve morphology HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0000775 Abnormality of the diaphragm skos:exactMatch 1 MP:0002279 abnormal diaphragm morphology HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0000778 Hypoplasia of the thymus skos:exactMatch 1 MP:0001823 thymus hypoplasia HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0000921 Missing ribs skos:exactMatch 1 MP:0003345 decreased rib number HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0001537 Umbilical hernia skos:exactMatch 1 MP:0010146 umbilical hernia HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0001696 Situs inversus totalis skos:exactMatch 1 MP:0011252 situs inversus totalis HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0001741 Phimosis skos:exactMatch 1 MP:0003554 phimosis HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0001943 Hypoglycemia skos:exactMatch 1 MP:0005560 decreased circulating glucose level HumanCurated orcid:0000-0003-4606-0597 1/27/2022 "the MP also has a term for hypoglycemia (child of decreased circulating glucose level) but states that this generally refers to the pathological state. Since the HPO terms is defined just as ""A decreased concentration of glucose in the blood."" I think the circulating term is a better match" +HP:0002020 Gastroesophageal reflux skos:exactMatch 1 MP:0003286 gastroesophageal reflux HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0002119 Ventriculomegaly skos:exactMatch 1 MP:0011380 enlarged brain ventricles HumanCurated orcid:0000-0003-4606-0597 1/28/2022 +HP:0002435 Meningocele skos:exactMatch 0.8 MP:0012259 meningocele HumanCurated orcid:0000-0003-4606-0597|orcid:0000-0002-6490-7723 1/28/2022 "the HPO definition specifies ""vertebral column"" but 2 of the children are for skull related defects. MP term specifies ""base of skull or gaps in vertebrae"" I think these are intended to be exact matches but definition issues contributes to uncertainty. Tabers definition has ""defect in skull spinal column""" +HP:0002808 Kyphosis skos:exactMatch 0.9 MP:0000160 kyphosis HumanCurated orcid:0000-0003-4606-0597 1/28/2022 +HP:0003298 Spina bifida occulta skos:exactMatch 1 MP:0005297 spina bifida occulta HumanCurated orcid:0000-0003-4606-0597 1/28/2022 +HP:0005107 Abnormal sacrum morphology skos:exactMatch 1 MP:0010113 abnormal sacrum morphology HumanCurated orcid:0000-0003-4606-0597 1/28/2022 MP defintion specifies that the sacrum occurs in humans and tailess primates but we have mouse annotations??? Possibly it would better to map to the more sacral vertebrae term? +HP:0005160 Total anomalous pulmonary venous return skos:exactMatch 1 MP:0010441 total anomalous pulmonary venous connection HumanCurated orcid:0000-0003-4606-0597 1/28/2022 +HP:0010773 Partial anomalous pulmonary venous return skos:exactMatch 1 MP:0010442 partial anomalous pulmonary venous connection HumanCurated orcid:0000-0003-4606-0597 2/2/2022 +HP:0011297 Abnormal digit morphology skos:exactMatch 1 MP:0002110 abnormal digit morphology HumanCurated orcid:0000-0003-4606-0597 2/2/2022 +HP:0011611 Interrupted aortic arch skos:exactMatch 1 MP:0004157 interrupted aortic arch HumanCurated orcid:0000-0003-4606-0597 2/2/2022 +HP:0012541 Cephalohematoma skos:exactMatch 1 MP:0001915 intracranial hemorrhage HumanCurated orcid:0000-0003-4606-0597 2/2/2022 +HP:0012795 Abnormality of the optic disc skos:exactMatch 1 MP:0008259 abnormal optic disk morphology HumanCurated orcid:0000-0003-4606-0597 2/2/2022 +HP:0030875 Abnormality of pulmonary circulation skos:exactMatch 1 MP:0002295 abnormal pulmonary circulation HumanCurated orcid:0000-0003-4606-0597 2/2/2022 +HP:0000039 Epispadias skos:exactMatch 1 MP:0003598 epispadia HumanCurated orcid:0000-0003-4606-0597|orcid:0000-0002-6490-7723 2/9/2022 These will be exact once the change to the HP definition goes through. The MP term is also incorrectly placed under abnormal penis morphology MP:0005187. This parent term has been removed (see MP issue #3512) +HP:0000048 Bifid scrotum skos:exactMatch 1 MP:0003612 bifid scrotum HumanCurated orcid:0000-0003-4606-0597 2/11/2022 +HP:0000086 Ectopic kidney skos:exactMatch 1 MP:0003600 ectopic kidney HumanCurated orcid:0000-0002-6490-7723 9/20/2021 MP term definition provides additional detail such as usual cause and sites of ectopic kidneys but terms are essentially equivalent; both MP and HPO terms use renal ectopia as an exact synonym +HP:0000105 Enlarged kidney skos:exactMatch 1 MP:0003068 enlarged kidney HumanCurated orcid:0000-0002-6490-7723 12/20/2021 +HP:0000125 Pelvic kidney skos:exactMatch 1 MP:0011361 pelvic kidney HumanCurated orcid:0000-0003-4606-0597 2/11/2022 add synonym +HP:0000268 Dolichocephaly skos:exactMatch 0.9 MP:0003742 narrow head HumanCurated orcid:0000-0003-4606-0597 2/11/2022 "while the MP term only refers to narrow, dolichocephaly is an exact synonym, uncertainty due to the lack of mention of increase in height" +HP:0000340 Sloping forehead skos:exactMatch 1 MP:0030048 sloping forehead HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 2/11/2022 "MP term definition is an exact match to the ""alternative"" HPO term definition" +HP:0000520 Proptosis skos:exactMatch 1 MP:0002750 exophthalmos HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 6/21/2022 +HP:0000527 Long eyelashes skos:exactMatch 1 MP:0031288 long eyelid cilia HumanCurated orcid:0000-0003-4606-0597 6/21/2022 MP term matches the subjective definition +HP:0000528 Anophthalmia skos:exactMatch 1 MP:0001293 anophthalmia HumanCurated orcid:0000-0003-4606-0597 6/21/2022 +HP:0000577 Exotropia skos:exactMatch 1 MP:0005255 exotropia HumanCurated orcid:0000-0003-4606-0597 6/21/2022 +HP:0000601 Hypotelorism skos:exactMatch 1 MP:0006197 ocular hypotelorism HumanCurated orcid:0000-0002-6490-7723 12/20/2021 +HP:0000648 Optic atrophy skos:exactMatch 1 MP:0001059 optic nerve atrophy HumanCurated orcid:0000-0003-4606-0597 7/26/2022 "MP term specifies ""acquired"" HPO does not mention this but both specify death of cells" +HP:0000807 Glandular hypospadias skos:exactMatch 0.8 MP:0031295 glanular hypospadia HumanCurated orcid:0000-0003-4606-0597 7/26/2022 uncertainty due to absence of definition in HPO but MGI synonym matches HPO term name +HP:0000808 Penoscrotal hypospadias skos:exactMatch 1 MP:0031296 penoscrotal hypospadia HumanCurated orcid:0000-0003-4606-0597 7/26/2022 +HP:0001388 Joint laxity skos:exactMatch 1 MP:0030797 joint laxity HumanCurated orcid:0000-0003-4606-0597 8/10/2022 +HP:0001902 Giant platelets skos:exactMatch 0.9 MP:0030025 giant platelets HumanCurated orcid:0000-0003-4606-0597 8/10/2022 "MP term matches the second part of the HPO definition ""as large as or larger than the red blood cells""" +HP:0002240 Hepatomegaly skos:exactMatch 1 MP:0000599 enlarged liver HumanCurated orcid:0000-0002-6490-7723 11/11/2021 +HP:0002904 Hyperbilirubinemia skos:exactMatch 1 MP:0005344 increased circulating bilirubin level HumanCurated orcid:0000-0002-6490-7723 11/11/2021 +HP:0002982 Tibial bowing skos:exactMatch 1 MP:0004358 bowed tibia HumanCurated orcid:0000-0002-6490-7723 11/11/2021 +HP:0000243 Trigonocephaly skos:exactMatch 1 MP:0030368 trigonocephaly HumanCurated orcid:0000-0002-6490-7723 8/10/2022 +HP:0000402 Stenosis of the external auditory canal skos:exactMatch 1 MP:0031285 external auditory canal stenosis HumanCurated orcid:0000-0002-6490-7723 5/27/2021 +HP:0000431 Wide nasal bridge skos:exactMatch 1 MP:0000449 broad nasal bridge HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 8/10/2022 both terms use the same logical definition so I think these are the same despite differences in the text definitions +HP:0000453 Choanal atresia skos:exactMatch 1 MP:0008970 choanal atresia HumanCurated orcid:0000-0002-6490-7723 9/20/2021 "MP definition specifies ""blockage of the back of the nasal passage by abnormal bony or soft tissue"" and additional detail on developmental cause. However, HPO term uses ""blockage"" and ""obstruction"" of the rear opening of the nasal cavity as exact synonyms, and both MP and HPO terms use atretic (= absence or abnormal closure) in the eqs so I think these are equivalent" +HP:0000698 Conical tooth skos:exactMatch 1 MP:0030499 conical tooth HumanCurated orcid:0000-0002-6490-7723 9/20/2021 +HP:0000787 Nephrolithiasis skos:exactMatch 1 MP:0002708 nephrolithiasis HumanCurated orcid:0000-0002-6490-7723 5/27/2021 +HP:0000958 Dry skin skos:exactMatch 1 MP:0003853 dry skin HumanCurated orcid:0000-0002-6490-7723 5/27/2021 +HP:0002777 Tracheal stenosis skos:exactMatch 1 MP:0010883 trachea stenosis HumanCurated orcid:0000-0002-6490-7723 9/20/2021 +HP:0002779 Tracheomalacia skos:exactMatch 1 MP:0013753 tracheomalacia HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 8/10/2022 HPO provides no textual definition (only synonym) match is based on xrefs of the HPO term as well as term name and synonym +HP:0007633 Bilateral microphthalmos skos:exactMatch 1 MP:0031290 bilateral microphthalmia HumanCurated orcid:0000-0002-6490-7723 9/20/2021 "new term, parent would be MP:0001297" +HP:0010478 Abnormality of the urachus skos:exactMatch 0.8 MP:0003616 abnormal urachus morphology HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 12/20/2021 "HPO provides no textual definition, placement in HPO would suggest this is morphology but the eq uses ""quality"" not ""morphology""" +HP:0011035 Abnormal renal cortex morphology skos:exactMatch 1 MP:0000521 abnormal kidney cortex morphology HumanCurated orcid:0000-0002-6490-7723 12/20/2021 +HP:0011390 Morphological abnormality of the inner ear skos:exactMatch 1 MP:0000026 abnormal inner ear morphology HumanCurated orcid:0000-0002-6490-7723 12/20/2021 +HP:0011892 Low levels of vitamin K skos:exactMatch 1 MP:0031263 decreased vitamin K level HumanCurated orcid:0000-0002-6490-7723 12/20/2021 +HP:0012211 Abnormal renal physiology skos:exactMatch 1 MP:0002136 abnormal kidney physiology HumanCurated orcid:0000-0002-6490-7723 12/20/2021 +HP:0025407 Rectourethral fistula skos:exactMatch 0 MP:0011786 rectourethral fistula HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 5/27/2021 +HP:0025426 Abnormal bronchus morphology skos:exactMatch 0 MP:0002264 abnormal bronchus morphology HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 5/27/2021 +HP:0100633 Esophagitis skos:exactMatch 1 MP:0003278 esophageal inflammation HumanCurated orcid:0000-0002-6490-7723 9/20/2021 +HP:0410030 Cleft lip skos:narrowMatch 1 MP:0005170 cleft upper lip HumanCurated orcid:0000-0003-4606-0597 5/27/2021 HP term applies to either upper or lower lip +HP:0000271 Abnormality of the face skos:narrowMatch 0.9 MP:0003743 abnormal facial morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 I think the HPO term is broader as it has children like rhinitis which we would not put under facial morphology +HP:0040064 Abnormality of limbs skos:narrowMatch 1 MP:0000546 abnormal limb morphology HumanCurated orcid:0000-0003-4606-0597 5/27/2021 MP has morphology term and a general limb/digit/tail phenotype term but not a general limb abnormality term (that would cover morphology and physiology) +HP:0000768 Pectus carinatum skos:narrowMatch 0.8 MP:0031277 pectus carinatum HumanCurated orcid:0000-0002-6490-7723 5/27/2021 "new child of MP:0004134; new MP term specifies congenital, HPO does not" +HP:0000104 Renal agenesis skos:narrowMatch 0.9 MP:0000520 absent kidney HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "absence of both kidneys, HPO term has child terms for bilateral and unilateral renal agenesis that would be exact matches to the MP terms" +HP:0000104 Renal agenesis skos:narrowMatch 0.9 MP:0003604 single kidney HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001642 Pulmonic stenosis skos:narrowMatch 1 MP:0006128 pulmonary valve stenosis HumanCurated orcid:0000-0003-4606-0597 8/10/2022 "MP refers only to the valve, HP is valve plus just below the pulmonary valve (infundibular stenosis). Comment on MP specifically excluded infundibular stenosis" +HP:0007033 Cerebellar dysplasia skos:narrowMatch 0.9 MP:0000854 abnormal cerebellum development HumanCurated orcid:0000-0003-4606-0597 7/15/2021 +HP:0000286 Epicanthus skos:narrowMatch 1 MP:0006168 epicanthus inversus HumanCurated orcid:0000-0003-4606-0597 1/25/2022 consider adding a new term for this that would be a parent to existing term +HP:0001743 Abnormality of the spleen skos:narrowMatch 1 MP:0000689 abnormal spleen morphology HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0001743 Abnormality of the spleen skos:narrowMatch 1 MP:0008737 abnormal spleen physiology HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0000464 Abnormality of the neck skos:narrowMatch 1 MP:0012719 abnormal neck morphology HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 2/11/2022 "MP term is limited to morphology, HPO term could refer to morphology or physiology" +HP:0000579 Nasolacrimal duct obstruction skos:narrowMatch 1 MP:0013451 nasolacrimal duct obstruction HumanCurated orcid:0000-0002-6490-7723 12/20/2021 MP term definition refers specifically to the nasolacrimal duct whereas the HPO definition refers to the lacrimal duct (According to Taber's a lacrimal duct is any of the small excretory ducts of the lacrimal glands) +HP:0010448 Colonic atresia skos:narrowMatch 1 MP:0031343 colon atresia HumanCurated orcid:0000-0002-6490-7723 12/20/2021 "MP term specifies congenital whereas HPO does not specify congenital and uses ""large intestine"" in exact synonyms" +HP:0011102 Ileal atresia skos:narrowMatch 1 MP:0011879 ileum atresia HumanCurated orcid:0000-0002-6490-7723 12/20/2021 "The MP term is more narrow as it specifies ""congenital blockage or absence of the lumen of the ileum""" +HP:0100542 Abnormal localization of kidney skos:narrowMatch 1 MP:0003600 ectopic kidney HumanCurated orcid:0000-0002-6490-7723 9/20/2021 Ectopic kidney HP:0000086 is a child term of Abnormal localization of kidney HP:0100542 +HP:0001710 Conotruncal defect skos:relatedMatch 0.9 MP:0006126 abnormal cardiac outflow tract development HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP has this as the process but not a general morphology term, possibly we should add one?" +HP:0000329 Facial hemangioma skos:relatedMatch 1 MP:0031292 increased facial hemangioma incidence HumanCurated orcid:0000-0002-6490-7723 4/11/2022 MP has increased hemangioma incidence (MP:0002947) and specific terms for retinal and oral mucosa. There is also a generic hemangioma term but I think that should be obsoleted. In general for tumors we have abnormal tumor incidence terms rather than just bare tumor terms. We could add an abnormal and/or increased facial hemangioma incidence terms +HP:0001067 Neurofibromas skos:relatedMatch 1 MP:0010314 increased neurofibroma incidence HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0005116 Arterial tortuosity skos:relatedMatch 0.9 MP:0031132 increased artery tortuosity HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "Possibly these could be considered exact, but MP allows for a baseline of tortuosity to exist and the the term covers only an increase relative to some control " +HP:0003006 Neuroblastoma skos:relatedMatch 1 MP:0002039 increased neuroblastoma incidence HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 5/27/2021 +HP:0030038 Enchondroma skos:relatedMatch 1 MP:0031283 increased enchondroma incidence HumanCurated orcid:0000-0002-6490-7723 5/27/2021 new incidence term falls under increased skeletal tumor incidence +HP:0001028 Hemangioma skos:relatedMatch 1 MP:0002947 increased hemangioma incidence HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0002672 Gastrointestinal carcinoma skos:relatedMatch 0.8 MP:0010279 increased gastrointestinal tumor incidence HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 5/27/2021 "MP term covers all types of GI tumors, not sure if related or broad is the better match term" +HP:0410264 Subglottic hemangioma skos:relatedMatch 0.8 MP:0002947 increased hemangioma incidence HumanCurated orcid:0000-0002-6490-7723|orcid:0000-0003-4606-0597 5/27/2021 "MP term covers all types of hemangiomas, not sure if related or broad is the better match term" +HP:0004322 Short stature skos:relatedMatch 0.9 MP:0001255 decreased body height HumanCurated orcid:0000-0003-4606-0597 5/27/2021 "MP height is defined as shoulder to floor while length is defined as head and trunk neither is quite the same as ""stature"" in human which I'm assuming is crown of head to floor" +HP:0004322 Short stature skos:relatedMatch 0.9 MP:0001258 decreased body length HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0030431 Osteochondroma skos:relatedMatch 1 MP:0010079 increased osteochondroma incidence HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0002895 Papillary thyroid carcinoma skos:relatedMatch 1 MP:0010346 increased thyroid carcinoma incidence HumanCurated orcid:0000-0003-4606-0597 5/27/2021 +HP:0001748 Polysplenia skos:relatedMatch 0.9 MP:0003342 accessory spleen HumanCurated orcid:0000-0003-4606-0597 5/27/2021 The HP has the parent term Supernumerary spleens (HP:0009799) and the sibling Accessory spleen (HP:0001747). None of the text definitions match what the MP has for accessory spleens +HP:0002744 Bilateral cleft lip and palate skos:relatedMatch 1 MP:0000111 cleft palate HumanCurated orcid:0000-0003-4606-0597 1/25/2022 "combination phenotype, should consider filling out this branch of MP" +HP:0002744 Bilateral cleft lip and palate skos:relatedMatch 1 MP:0005170 cleft upper lip HumanCurated orcid:0000-0003-4606-0597 1/25/2022 +HP:0006743 Embryonal rhabdomyosarcoma skos:relatedMatch 1 MP:0002036 increased rhabdomyosarcoma incidence HumanCurated orcid:0000-0003-4606-0597 1/25/2022 +HP:0030434 Pilomatrixoma skos:relatedMatch 1 MP:0002013 increased pilomatricoma incidence HumanCurated orcid:0000-0003-4606-0597 1/27/2022 +HP:0005107 Abnormal sacrum morphology skos:relatedMatch 1 MP:0003050 abnormal sacral vertebrae morphology HumanCurated orcid:0000-0003-4606-0597 1/31/2022 +HP:0010305 Absence of the sacrum skos:relatedMatch 1 MP:0004656 absent sacral vertebrae HumanCurated orcid:0000-0003-4606-0597 1/31/2022 +HP:0010796 Brainstem glioma skos:relatedMatch 0.8 MP:0010278 increased glioma incidence HumanCurated orcid:0000-0003-4606-0597 2/2/2022 "this is both broad and related, possibly we should add a term for brain glioma incidence to get a closer term" +HP:0012189 Hodgkin lymphoma skos:relatedMatch 0.8 MP:0012431 increased lymphoma incidence HumanCurated orcid:0000-0003-4606-0597 2/2/2022 "both broad and related, single annotation to this term that mentions Hodgkin's multiple ones mention non-Hodgkin's" +HP:0012254 Ewing sarcoma skos:relatedMatch 0.8 MP:0002032 increased sarcoma incidence HumanCurated orcid:0000-0003-4606-0597 2/2/2022 "both broad and related, no annotations in MGI " +HP:0100777 Exostoses skos:relatedMatch 0.8 MP:0010280 increased skeletal tumor incidence HumanCurated orcid:0000-0003-4606-0597 2/2/2022 "broad and related, consider adding new term MGI does have annotations to hereditary multiple exostoses but these are annotated to increased osteochondroma incidence " +HP:0410271 Laryngeal hemangioma skos:relatedMatch 1 MP:0002947 increased hemangioma incidence HumanCurated orcid:0000-0003-4606-0597 2/7/2022 "both broad and related, no annotations in MGI " +HP:0410275 Lumbosacral hemangioma skos:relatedMatch 1 MP:0002947 increased hemangioma incidence HumanCurated orcid:0000-0003-4606-0597 2/7/2022 "both broad and related, no annotations in MGI " +HP:0000219 Thin upper lip vermilion skos:relatedMatch 1 MP:0030168 thin upper lip HumanCurated orcid:0000-0003-4606-0597 2/11/2022 +HP:0000739 Anxiety skos:relatedMatch 1 MP:0001363 increased anxiety-related response HumanCurated orcid:0000-0002-6490-7723 5/27/2021 +HP:0002860 Squamous cell carcinoma skos:relatedMatch 1 MP:0009704 increased skin squamous cell carcinoma incidence HumanCurated orcid:0000-0002-6490-7723 9/20/2021 +HP:0002890 Thyroid carcinoma skos:relatedMatch 1 MP:0010346 increased thyroid carcinoma incidence HumanCurated orcid:0000-0002-6490-7723 9/20/2021 +HP:0003003 Colon cancer skos:relatedMatch 1 MP:0012436 increased colon tumor incidence HumanCurated orcid:0000-0002-6490-7723 9/20/2021 +HP:0003005 Ganglioneuroma skos:relatedMatch 1 MP:0010362 increased ganglioneuroma incidence HumanCurated orcid:0000-0002-6490-7723 9/20/2021 MP term definition is based on MPATH:375 and does not specify where ganglioneuroma arises +HP:0006687 Aortic tortuosity skos:relatedMatch 0.9 MP:0031133 increased aorta tortuosity HumanCurated orcid:0000-0002-6490-7723 12/20/2021 Possibly exact but the MP term allows for a baseline of tortuosity to exist and the term covers only an increase relative to some control +HP:0009792 Teratoma skos:relatedMatch 1 MP:0002627 increased teratoma incidence HumanCurated orcid:0000-0002-6490-7723 12/20/2021 HPO does not actually define teratoma whereas MP does +HP:0010614 Fibroma skos:relatedMatch 1 MP:0003580 increased fibroma incidence HumanCurated orcid:0000-0002-6490-7723 12/20/2021 +HP:0012226 Ovarian teratoma skos:relatedMatch 1 MP:0009442 increased ovarian teratoma incidence HumanCurated orcid:0000-0002-6490-7723 12/20/2021 diff --git a/tests/test_validate.py b/tests/test_validate.py index 05d695e5..145ef1fd 100644 --- a/tests/test_validate.py +++ b/tests/test_validate.py @@ -6,6 +6,7 @@ from sssom.constants import DEFAULT_VALIDATION_TYPES, SchemaValidationType from sssom.parsers import parse_sssom_table +from sssom.util import SssomMalformedYamlError from sssom.validators import validate from tests.constants import data_dir @@ -61,3 +62,16 @@ def test_validate_sparql(self): self.correct_msdf1, self.shacl_validation_types, ) + + def test_validate_json_fail_mgi(self): + """ + Test if JSONSchemaValidation fail is as expected. + + In this particular test case, the 'mapping_justification' slot + does not have EntityReference objects, but strings. + """ + self.assertRaises( + SssomMalformedYamlError, + parse_sssom_table, + f"{data_dir}/hp_mp_kidsfirst_mgi.sssom.tsv", + )