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monarch-initiative / mondo

Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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Add defs+references for newly added rare disease terms #79

Closed cmungall closed 2 years ago

cmungall commented 6 years ago

use a sparql query to find all text-definition less terms, prioritize ones in gard_rare subset

nicolevasilevsky commented 6 years ago

Sure thing.

If the MONDO term xrefs another ontology and there is a def in the other ontology, should I just use that def?

For example, MONDO_0016659 '8p23.1 duplication syndrome' xrefs Orphanet:251076 and there is a def on the Orphanet page: http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=251076

Should I use this Orphanet definition on the MONDO term?

cmungall commented 6 years ago

I would focus on those without an orphanet xref. We will bring in orphanet defs automatically next orphanet release.

(ORDO lags behind the site by 6 months)

nicolevasilevsky commented 6 years ago

@cmungall I am trying to do a pull request, but am getting crazy diffs again:

Last login: Mon Feb 12 09:26:13 on ttys000 BICB119:~ vasilevs$ ls Applications My Cloud Books Pictures Box Sync Public CmapToolsLogs README.md Desktop Robot Documents SplicingProject Downloads bin Dropbox git Google Drive git.datawebsite-delete-me Library igv Movies oboedit_config Music svn BICB119:~ vasilevs$ cd git/mondo-build/src/ontology BICB119:ontology vasilevs$ BICB119:ontology vasilevs$ git status On branch issue-79 nothing to commit, working tree clean BICB119:ontology vasilevs$ git checkout master Switched to branch 'master' Your branch is up-to-date with 'origin/master'. BICB119:ontology vasilevs$ git pull Already up-to-date. BICB119:ontology vasilevs$ git checkout issue-79 Switched to branch 'issue-79' BICB119:ontology vasilevs$ git status On branch issue-79 nothing to commit, working tree clean BICB119:ontology vasilevs$ git diff diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index e5949b2..71d0bc4 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -3,8 +3,8 @@ subsetdef: clingen "initial subset used by clingen" subsetdef: do_inheritance_inconsistent "classes where the corresponding DO term is both AR and AD https://github.com/monarch-initiative/monarch-disease-ontology/issues/406" subsetdef: gard_rare "GARD rare disease subset" subsetdef: merged_class "this class merges distinct concepts in other resources" -subsetdef: not_a_disease "classes that do not represent diseases" subsetdef: n_of_one "N of one" +subsetdef: not_a_disease "classes that do not represent diseases" subsetdef: ordo_biological_anomaly "biological anomaly" subsetdef: ordo_clinical_situation "particular clinical situation in a disease or syndrome" subsetdef: ordo_clinical_subtype "clinical subtype" @@ -1929,9 +1929,9 @@ synonym: "Rickettsia africae spotted fever" EXACT [DOID:0050035] synonym: "South African tick-bite fever" EXACT [DOID:0050035] xref: DOID:0050035 {source="MONDO:Leader", source="MONDO:equivalentTo"} is_a: MONDO:0001195 {source="DOID:0050035"} ! spotted fever -relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae intersection_of: MONDO:0001195 ! spotted fever intersection_of: transmitted_by NCBITaxon:6942 ! Amblyomma +relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae

[Term] id: MONDO:0000228 @@ -2479,7 +2479,7 @@ id: MONDO:0000276 name: Powassan encephalitis def: "A viral infectious disease that results_in inflammation located_in brain, has_material_basis_in Powassan virus, which is transmitted_by Ixodes and transmitted_by Dermacentor species of ticks. The infection has_symptom headache, has_symptom fever, has_symptom vomiting, has_symptom stiff neck, has_symptom sleepiness, has_symptom breathing distress, has_symptom tremors, has_symptom confusion, : or syndrome" subsetdef: ordo_clinical_subtype "clinical subtype" @@ -1929,9 +1929,9 @@ synonym: "Rickettsia africae spotted fever" EXACT [DOID:0050035] synonym: "South African tick-bite fever" EXACT [DOID:0050035] xref: DOID:0050035 {source="MONDO:Leader", source="MONDO:equivalentTo"} is_a: MONDO:0001195 {source="DOID:0050035"} ! spotted fever -relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae intersection_of: MONDO:0001195 ! spotted fever intersection_of: transmitted_by NCBITaxon:6942 ! Amblyomma +relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae

[Term] id: MONDO:0000228 @@ -2479,7 +2479,7 @@ id: MONDO:0000276 name: Powassan encephalitis def: "A viral infectious disease that results_in inflammation located_in brain, has_material_basis_in Powassan virus, which is transmitted_by Ixodes and transmitted_by Dermacentor species of ticks. The infection has_symptom headache, has_symptom fever, has_symptom vomiting, has_symptom stiff neck, has_symptom sleepiness, has_symptom breathing distress, has_symptom tremors, has_symptom confusion, has_symptom seizures, has_symptom paralysis, and has_symptom coma." [DOID:0050179, http://chppm-www.apgea.army.mil/ento/facts/Powassan-JusttheFactsJanuary2004.pdf] xref: DOID:0050179 {source="MONDO:Leader", source="MONDO:equivalentTo"} -xref: SCTID:416707008 {source="MONDO:equivalentTo"} ! powassan encephalitis vir: or syndrome" subsetdef: ordo_clinical_subtype "clinical subtype" @@ -1929,9 +1929,9 @@ synonym: "Rickettsia africae spotted fever" EXACT [DOID:0050035] synonym: "South African tick-bite fever" EXACT [DOID:0050035] xref: DOID:0050035 {source="MONDO:Leader", source="MONDO:equivalentTo"} is_a: MONDO:0001195 {source="DOID:0050035"} ! spotted fever -relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae intersection_of: MONDO:0001195 ! spotted fever intersection_of: transmitted_by NCBITaxon:6942 ! Amblyomma +relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae

[Term] id: MONDO:0000228 @@ -2479,7 +2479,7 @@ id: MONDO:0000276 name: Powassan encephalitis def: "A viral infectious disease that results_in inflammation located_in brain, has_material_basis_in Powassan virus, which is transmitted_by Ixodes and transmitted_by Dermacentor species of ticks. The infection has_symptom headache, has_symptom fever, has_symptom vomiting, has_symptom stiff neck, has_symptom sleepiness, has_symptom breathing distress, has_symptom tremors, has_symptom confusion, has_symptom seizures, has_symptom paralysis, and has_symptom coma." [DOID:0050179, http://chppm-www.apgea.army.mil/ento/facts/Powassan-JusttheFactsJanuary2004.pdf] xref: DOID:0050179 {source="MONDO:Leader", source="MONDO:equivalentTo"} -xref: SCTID:416707008 {source="MONDO:equivalentTo"} ! powassan encephalitis virus infection +xref: SCTID:416707008 {source="MONDO:equivalentTo"} is_a: MONDO:0002645 {source="OWLReasoner:2017"} ! cerebritis is_a: MONDO:0006009 {source="OWLReasoner:Elk-2018-01-21"} ! viral encephalitis is_a: MONDO:0015576 {source="OWLReasoner:2017"} ! rare viral disease @@ -6043,11 +6043,11 @@ is_a: MONDO:0002025 {source="MESH:D010262"} ! disease of: or syndrome" subsetdef: ordo_clinical_subtype "clinical subtype" @@ -1929,9 +1929,9 @@ synonym: "Rickettsia africae spotted fever" EXACT [DOID:0050035] synonym: "South African tick-bite fever" EXACT [DOID:0050035] xref: DOID:0050035 {source="MONDO:Leader", source="MONDO:equivalentTo"} is_a: MONDO:0001195 {source="DOID:0050035"} ! spotted fever -relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae intersection_of: MONDO:0001195 ! spotted fever intersection_of: transmitted_by NCBITaxon:6942 ! Amblyomma +relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae

[Term] id: MONDO:0000228 @@ -2479,7 +2479,7 @@ id: MONDO:0000276 name: Powassan encephalitis def: "A viral infectious disease that results_in inflammation located_in brain, has_material_basis_in Powassan virus, which is transmitted_by Ixodes and transmitted_by Dermacentor species of ticks. The infection has_symptom headache, has_symptom fever, has_symptom vomiting, has_symptom stiff neck, has_symptom sleepiness, has_symptom breathing distress, has_symptom tremors, has_symptom confusion, has_symptom seizures, has_symptom paralysis, and has_symptom coma." [DOID:0050179, http://chppm-www.apgea.army.mil/ento/facts/Powassan-JusttheFactsJanuary2004.pdf] xref: DOID:0050179 {source="MONDO:Leader", source="MONDO:equivalentTo"} -xref: SCTID:416707008 {source="MONDO:equivalentTo"} ! powassan encephalitis virus infection +xref: SCTID:416707008 {source="MONDO:equivalentTo"} is_a: MONDO:0002645 {source="OWLReasoner:2017"} ! cerebritis is_a: MONDO:0006009 {source="OWLReasoner:Elk-2018-01-21"} ! viral encephalitis is_a: MONDO:0015576 {source="OWLReasoner:2017"} ! rare viral disease @@ -6043,11 +6043,11 @@ is_a: MONDO:0002025 {source="MESH:D010262"} ! disease of mental health id: MONDO:0000597 name: Munchausen by proxy : or syndrome" subsetdef: ordo_clinical_subtype "clinical subtype" @@ -1929,9 +1929,9 @@ synonym: "Rickettsia africae spotted fever" EXACT [DOID:0050035] synonym: "South African tick-bite fever" EXACT [DOID:0050035] xref: DOID:0050035 {source="MONDO:Leader", source="MONDO:equivalentTo"} is_a: MONDO:0001195 {source="DOID:0050035"} ! spotted fever -relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae intersection_of: MONDO:0001195 ! spotted fever intersection_of: transmitted_by NCBITaxon:6942 ! Amblyomma +relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae

[Term] id: MONDO:0000228 @@ -2479,7 +2479,7 @@ id: MONDO:0000276 name: Powassan encephalitis def: "A viral infectious disease that results_in inflammation located_in brain, has_material_basis_in Powassan virus, which is transmitted_by Ixodes and transmitted_by Dermacentor species of ticks. The infection has_symptom headache, has_symptom fever, has_symptom vomiting, has_symptom stiff neck, has_symptom sleepiness, has_symptom breathing distress, has_symptom tremors, has_symptom confusion, has_symptom seizures, has_symptom paralysis, and has_symptom coma." [DOID:0050179, http://chppm-www.apgea.army.mil/ento/facts/Powassan-JusttheFactsJanuary2004.pdf] xref: DOID:0050179 {source="MONDO:Leader", source="MONDO:equivalentTo"} -xref: SCTID:416707008 {source="MONDO:equivalentTo"} ! powassan encephalitis virus infection +xref: SCTID:416707008 {source="MONDO:equivalentTo"} is_a: MONDO:0002645 {source="OWLReasoner:2017"} ! cerebritis is_a: MONDO:0006009 {source="OWLReasoner:Elk-2018-01-21"} ! viral encephalitis is_a: MONDO:0015576 {source="OWLReasoner:2017"} ! rare viral disease @@ -6043,11 +6043,11 @@ is_a: MONDO:0002025 {source="MESH:D010262"} ! disease of mental health id: MONDO:0000597 name: Munchausen by proxy def: "A factitious disorder that involves a care giver's deliberate exaggeratio: or syndrome" subsetdef: ordo_clinical_subtype "clinical subtype" @@ -1929,9 +1929,9 @@ synonym: "Rickettsia africae spotted fever" EXACT [DOID:0050035] synonym: "South African tick-bite fever" EXACT [DOID:0050035] xref: DOID:0050035 {source="MONDO:Leader", source="MONDO:equivalentTo"} is_a: MONDO:0001195 {source="DOID:0050035"} ! spotted fever -relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae intersection_of: MONDO:0001195 ! spotted fever intersection_of: transmitted_by NCBITaxon:6942 ! Amblyomma +relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae

[Term] id: MONDO:0000228 @@ -2479,7 +2479,7 @@ id: MONDO:0000276 name: Powassan encephalitis def: "A viral infectious disease that results_in inflammation located_in brain, has_material_basis_in Powassan virus, which is transmitted_by Ixodes and transmitted_by Dermacentor species of ticks. The infection has_symptom headache, has_symptom fever, has_symptom vomiting, has_symptom stiff neck, has_symptom sleepiness, has_symptom breathing distress, has_symptom tremors, has_symptom confusion, has_symptom seizures, has_symptom paralysis, and has_symptom coma." [DOID:0050179, http://chppm-www.apgea.army.mil/ento/facts/Powassan-JusttheFactsJanuary2004.pdf] xref: DOID:0050179 {source="MONDO:Leader", source="MONDO:equivalentTo"} -xref: SCTID:416707008 {source="MONDO:equivalentTo"} ! powassan encephalitis virus infection +xref: SCTID:416707008 {source="MONDO:equivalentTo"} is_a: MONDO:0002645 {source="OWLReasoner:2017"} ! cerebritis is_a: MONDO:0006009 {source="OWLReasoner:Elk-2018-01-21"} ! viral encephalitis is_a: MONDO:0015576 {source="OWLReasoner:2017"} ! rare viral disease @@ -6043,11 +6043,11 @@ is_a: MONDO:0002025 {source="MESH:D010262"} ! disease of mental health id: MONDO:0000597 name: Munchausen by proxy def: "A factitious disorder that involves a care giver's deliberate exaggeration, fabrication, and/or induce physical, psychological, behavioral, and/or mental health problems in others." [DOID:0060045, http://en.wikipedia.org/wiki/Munchau: or syndrome" subsetdef: ordo_clinical_subtype "clinical subtype" @@ -1929,9 +1929,9 @@ synonym: "Rickettsia africae spotted fever" EXACT [DOID:0050035] synonym: "South African tick-bite fever" EXACT [DOID:0050035] xref: DOID:0050035 {source="MONDO:Leader", source="MONDO:equivalentTo"} is_a: MONDO:0001195 {source="DOID:0050035"} ! spotted fever -relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae intersection_of: MONDO:0001195 ! spotted fever intersection_of: transmitted_by NCBITaxon:6942 ! Amblyomma +relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae

[Term] id: MONDO:0000228 @@ -2479,7 +2479,7 @@ id: MONDO:0000276 name: Powassan encephalitis def: "A viral infectious disease that results_in inflammation located_in brain, has_material_basis_in Powassan virus, which is transmitted_by Ixodes and transmitted_by Dermacentor species of ticks. The infection has_symptom headache, has_symptom fever, has_symptom vomiting, has_symptom stiff neck, has_symptom sleepiness, has_symptom breathing distress, has_symptom tremors, has_symptom confusion, has_symptom seizures, has_symptom paralysis, and has_symptom coma." [DOID:0050179, http://chppm-www.apgea.army.mil/ento/facts/Powassan-JusttheFactsJanuary2004.pdf] xref: DOID:0050179 {source="MONDO:Leader", source="MONDO:equivalentTo"} -xref: SCTID:416707008 {source="MONDO:equivalentTo"} ! powassan encephalitis virus infection +xref: SCTID:416707008 {source="MONDO:equivalentTo"} is_a: MONDO:0002645 {source="OWLReasoner:2017"} ! cerebritis is_a: MONDO:0006009 {source="OWLReasoner:Elk-2018-01-21"} ! viral encephalitis is_a: MONDO:0015576 {source="OWLReasoner:2017"} ! rare viral disease @@ -6043,11 +6043,11 @@ is_a: MONDO:0002025 {source="MESH:D010262"} ! disease of mental health id: MONDO:0000597 name: Munchausen by proxy def: "A factitious disorder that involves a care giver's deliberate exaggeration, fabrication, and/or induce physical, psychological, behavioral, and/or mental health problems in others." [DOID:0060045, http://en.wikipedia.org/wiki/Munchausen_by_proxy] +subset: gard_rare +synonym: "Munchausen syndrome by proxy" RELATED [GARD:0007117] xref: DOID:0060045 {source="MONDO:Leader", source="MONDO:equivalentTo"} : or syndrome" subsetdef: ordo_clinical_subtype "clinical subtype" @@ -1929,9 +1929,9 @@ synonym: "Rickettsia africae spotted fever" EXACT [DOID:0050035] synonym: "South African tick-bite fever" EXACT [DOID:0050035] xref: DOID:0050035 {source="MONDO:Leader", source="MONDO:equivalentTo"} is_a: MONDO:0001195 {source="DOID:0050035"} ! spotted fever -relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae intersection_of: MONDO:0001195 ! spotted fever intersection_of: transmitted_by NCBITaxon:6942 ! Amblyomma +relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae

[Term] id: MONDO:0000228 @@ -2479,7 +2479,7 @@ id: MONDO:0000276 name: Powassan encephalitis def: "A viral infectious disease that results_in inflammation located_in brain, has_material_basis_in Powassan virus, which is transmitted_by Ixodes and transmitted_by Dermacentor species of ticks. The infection has_symptom headache, has_symptom fever, has_symptom vomiting, has_symptom stiff neck, has_symptom sleepiness, has_symptom breathing distress, has_symptom tremors, has_symptom confusion, has_symptom seizures, has_symptom paralysis, and has_symptom coma." [DOID:0050179, http://chppm-www.apgea.army.mil/ento/facts/Powassan-JusttheFactsJanuary2004.pdf] xref: DOID:0050179 {source="MONDO:Leader", source="MONDO:equivalentTo"} -xref: SCTID:416707008 {source="MONDO:equivalentTo"} ! powassan encephalitis virus infection +xref: SCTID:416707008 {source="MONDO:equivalentTo"} is_a: MONDO:0002645 {source="OWLReasoner:2017"} ! cerebritis is_a: MONDO:0006009 {source="OWLReasoner:Elk-2018-01-21"} ! viral encephalitis is_a: MONDO:0015576 {source="OWLReasoner:2017"} ! rare viral disease @@ -6043,11 +6043,11 @@ is_a: MONDO:0002025 {source="MESH:D010262"} ! disease of mental health id: MONDO:0000597 name: Munchausen by proxy def: "A factitious disorder that involves a care giver's deliberate exaggeration, fabrication, and/or induce physical, psychological, behavioral, and/or mental health problems in others." [DOID:0060045, http://en.wikipedia.org/wiki/Munchausen_by_proxy] +subset: gard_rare +synonym: "Munchausen syndrome by proxy" RELATED [GARD:0007117] xref: DOID:0060045 {source="MONDO:Leader", source="MONDO:equivalentTo"} -subset: gard_rare -synonym: "Munchausen syndrome by proxy" RELATED [GARD:0007117] +xref: GARD:0007117 {source="MONDO:equivalentTo"} xref: UMLS:C0085277 {source="GARD:0007117"} -xref: GARD:0007117 {source="MONDO:equivalentTo"} ! munchausen by proxy syndrome is_a: MONDO:0002103 {source="DOID:0060045"} ! factitious disorder

[Term] @@ -17267,21 +17267,21 @@ relationship: disease_has_location UBERON:0002185 {source="OWLReasoner:Elk-2018" : or syndrome" subsetdef: ordo_clinical_subtype "clinical subtype" @@ -1929,9 +1929,9 @@ synonym: "Rickettsia africae spotted fever" EXACT [DOID:0050035] synonym: "South African tick-bite fever" EXACT [DOID:0050035] xref: DOID:0050035 {source="MONDO:Leader", source="MONDO:equivalentTo"} is_a: MONDO:0001195 {source="DOID:0050035"} ! spotted fever -relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae intersection_of: MONDO:0001195 ! spotted fever intersection_of: transmitted_by NCBITaxon:6942 ! Amblyomma +relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae

[Term] id: MONDO:0000228 @@ -2479,7 +2479,7 @@ id: MONDO:0000276 name: Powassan encephalitis def: "A viral infectious disease that results_in inflammation located_in brain, has_material_basis_in Powassan virus, which is transmitted_by Ixodes and transmitted_by Dermacentor species of ticks. The infection has_symptom headache, has_symptom fever, has_symptom vomiting, has_symptom stiff neck, has_symptom sleepiness, has_symptom breathing distress, has_symptom tremors, has_symptom confusion, has_symptom seizures, has_symptom paralysis, and has_symptom coma." [DOID:0050179, http://chppm-www.apgea.army.mil/ento/facts/Powassan-JusttheFactsJanuary2004.pdf] xref: DOID:0050179 {source="MONDO:Leader", source="MONDO:equivalentTo"} -xref: SCTID:416707008 {source="MONDO:equivalentTo"} ! powassan encephalitis virus infection +xref: SCTID:416707008 {source="MONDO:equivalentTo"} is_a: MONDO:0002645 {source="OWLReasoner:2017"} ! cerebritis is_a: MONDO:0006009 {source="OWLReasoner:Elk-2018-01-21"} ! viral encephalitis is_a: MONDO:0015576 {source="OWLReasoner:2017"} ! rare viral disease @@ -6043,11 +6043,11 @@ is_a: MONDO:0002025 {source="MESH:D010262"} ! disease of mental health id: MONDO:0000597 name: Munchausen by proxy def: "A factitious disorder that involves a care giver's deliberate exaggeration, fabrication, and/or induce physical, psychological, behavioral, and/or mental health problems in others." [DOID:0060045, http://en.wikipedia.org/wiki/Munchausen_by_proxy] +subset: gard_rare +synonym: "Munchausen syndrome by proxy" RELATED [GARD:0007117] xref: DOID:0060045 {source="MONDO:Leader", source="MONDO:equivalentTo"} -subset: gard_rare -synonym: "Munchausen syndrome by proxy" RELATED [GARD:0007117] +xref: GARD:0007117 {source="MONDO:equivalentTo"} xref: UMLS:C0085277 {source="GARD:0007117"} -xref: GARD:0007117 {source="MONDO:equivalentTo"} ! munchausen by proxy syndrome is_a: MONDO:0002103 {source="DOID:0060045"} ! factitious disorder

[Term] @@ -17267,21 +17267,21 @@ relationship: disease_has_location UBERON:0002185 {source="OWLReasoner:Elk-2018" id: MONDO:0001359 name: Kohler's disease : or syndrome" subsetdef: ordo_clinical_subtype "clinical subtype" @@ -1929,9 +1929,9 @@ synonym: "Rickettsia africae spotted fever" EXACT [DOID:0050035] synonym: "South African tick-bite fever" EXACT [DOID:0050035] xref: DOID:0050035 {source="MONDO:Leader", source="MONDO:equivalentTo"} is_a: MONDO:0001195 {source="DOID:0050035"} ! spotted fever -relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae intersection_of: MONDO:0001195 ! spotted fever intersection_of: transmitted_by NCBITaxon:6942 ! Amblyomma +relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae

[Term] id: MONDO:0000228 @@ -2479,7 +2479,7 @@ id: MONDO:0000276 name: Powassan encephalitis def: "A viral infectious disease that results_in inflammation located_in brain, has_material_basis_in Powassan virus, which is transmitted_by Ixodes and transmitted_by Dermacentor species of ticks. The infection has_symptom headache, has_symptom fever, has_symptom vomiting, has_symptom stiff neck, has_symptom sleepiness, has_symptom breathing distress, has_symptom tremors, has_symptom confusion, has_symptom seizures, has_symptom paralysis, and has_symptom coma." [DOID:0050179, http://chppm-www.apgea.army.mil/ento/facts/Powassan-JusttheFactsJanuary2004.pdf] xref: DOID:0050179 {source="MONDO:Leader", source="MONDO:equivalentTo"} -xref: SCTID:416707008 {source="MONDO:equivalentTo"} ! powassan encephalitis virus infection +xref: SCTID:416707008 {source="MONDO:equivalentTo"} is_a: MONDO:0002645 {source="OWLReasoner:2017"} ! cerebritis is_a: MONDO:0006009 {source="OWLReasoner:Elk-2018-01-21"} ! viral encephalitis is_a: MONDO:0015576 {source="OWLReasoner:2017"} ! rare viral disease @@ -6043,11 +6043,11 @@ is_a: MONDO:0002025 {source="MESH:D010262"} ! disease of mental health id: MONDO:0000597 name: Munchausen by proxy def: "A factitious disorder that involves a care giver's deliberate exaggeration, fabrication, and/or induce physical, psychological, behavioral, and/or mental health problems in others." [DOID:0060045, http://en.wikipedia.org/wiki/Munchausen_by_proxy] +subset: gard_rare +synonym: "Munchausen syndrome by proxy" RELATED [GARD:0007117] xref: DOID:0060045 {source="MONDO:Leader", source="MONDO:equivalentTo"} -subset: gard_rare -synonym: "Munchausen syndrome by proxy" RELATED [GARD:0007117] +xref: GARD:0007117 {source="MONDO:equivalentTo"} xref: UMLS:C0085277 {source="GARD:0007117"} -xref: GARD:0007117 {source="MONDO:equivalentTo"} ! munchausen by proxy syndrome is_a: MONDO:0002103 {source="DOID:0060045"} ! factitious disorder

[Term] @@ -17267,21 +17267,21 @@ relationship: disease_has_location UBERON:0002185 {source="OWLReasoner:Elk-2018" id: MONDO:0001359 name: Kohler's disease def: "Kohler disease is a condition that affects a bone at the arch of the foot calle: or syndrome" subsetdef: ordo_clinical_subtype "clinical subtype" @@ -1929,9 +1929,9 @@ synonym: "Rickettsia africae spotted fever" EXACT [DOID:0050035] synonym: "South African tick-bite fever" EXACT [DOID:0050035] xref: DOID:0050035 {source="MONDO:Leader", source="MONDO:equivalentTo"} is_a: MONDO:0001195 {source="DOID:0050035"} ! spotted fever -relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae intersection_of: MONDO:0001195 ! spotted fever intersection_of: transmitted_by NCBITaxon:6942 ! Amblyomma +relationship: realized_in_response_to_stimulus NCBITaxon:35788 ! Rickettsia africae

[Term] id: MONDO:0000228 @@ -2479,7 +2479,7 @@ id: MONDO:0000276 name: Powassan encephalitis def: "A viral infectious disease that results_in inflammation located_in brain, has_material_basis_in Powassan virus, which is transmitted_by Ixodes and transmitted_by Dermacentor species of ticks. The infection has_symptom headache, has_symptom fever, has_symptom vomiting, has_symptom stiff neck, has_symptom sleepiness, has_symptom breathing distress, has_symptom tremors, has_symptom confusion, has_symptom seizures, has_symptom paralysis, and has_symptom coma." [DOID:0050179, http://chppm-www.apgea.army.mil/ento/facts/Powassan-JusttheFactsJanuary2004.pdf] xref: DOID:0050179 {source="MONDO:Leader", source="MONDO:equivalentTo"} -xref: SCTID:416707008 {source="MONDO:equivalentTo"} ! powassan encephalitis virus infection +xref: SCTID:416707008 {source="MONDO:equivalentTo"} is_a: MONDO:0002645 {source="OWLReasoner:2017"} ! cerebritis is_a: MONDO:0006009 {source="OWLReasoner:Elk-2018-01-21"} ! viral encephalitis is_a: MONDO:0015576 {source="OWLReasoner:2017"} ! rare viral disease @@ -6043,11 +6043,11 @@ is_a: MONDO:0002025 {source="MESH:D010262"} ! disease of mental health id: MONDO:0000597 name: Munchausen by proxy def: "A factitious disorder that involves a care giver's deliberate exaggeration, fabrication, and/or induce physical, psychological, behavioral, and/or mental health problems in others." [DOID:0060045, http://en.wikipedia.org/wiki/Munchausen_by_proxy] +subset: gard_rare +synonym: "Munchausen syndrome by proxy" RELATED [GARD:0007117] xref: DOID:0060045 {source="MONDO:Leader", source="MONDO:equivalentTo"} -subset: gard_rare -synonym: "Munchausen syndrome by proxy" RELATED [GARD:0007117] +xref: GARD:0007117 {source="MONDO:equivalentTo"} xref: UMLS:C0085277 {source="GARD:0007117"} -xref: GARD:0007117 {source="MONDO:equivalentTo"} ! munchausen by proxy syndrome is_a: MONDO:0002103 {source="DOID:0060045"} ! factitious disorder

[Term] @@ -17267,21 +17267,21 @@ relationship: disease_has_location UBERON:0002185 {source="OWLReasoner:Elk-2018" id: MONDO:0001359 name: Kohler's disease def: "Kohler disease is a condition that affects a bone at the arch of the foot called the tarsal navicular bone. X-rays show that this bone is initially compressed and later breaks into pieces before healing and hardening back into bone.It occurs most freq:

nicolevasilevsky commented 6 years ago

@cmungall and @GARDInfoCenter: for some diseases, I am unable to find any results in PubMed. I enlisted the help of Rose, our resident expert librarian to help me with some of the searches. She has sent me a number of references to look through for some diseases, but upon first glance, I think there may be some diseases where there is no literature available in PubMed.

Some examples of diseases where I cannot find a reference/definition are below:

Thanks!

GARDInfoCenter commented 6 years ago

GARD staff will research on our end to see what we find regarding these diseases.

GARDInfoCenter commented 6 years ago

Aluminium lung is characterized as diffuse interstitial fibrosis which is mainly located in the upper and middle lobes of the lung. In advanced stages it is characterized by subpleural bullous emphysema with an increased risk of spontaneous pneumothorax [5]. The prognosis for severe forms of lung fibrosis is poor because the disease can continue to progress after the end of exposure. Therefore early detection of aluminium induced fibrotic changes is invaluable to the timely introduction of preventative measures. Early stage lung changes, induced by aluminium dust, could not be diagnosed to date using conventional X-rays in several cross-sectional studies in the aluminium powder industry [9] or during general occupational medical surveillance. https://occup-med.biomedcentral.com/articles/10.1186/1745-6673-1-4

https://www.ncbi.nlm.nih.gov/pubmed/?term=%22aluminum+lung%22

GARDInfoCenter commented 6 years ago

Goralewski and Jaeger2 also described a similar pattern of pulmonary fibrosis, which they referred to as “aluminiumlunge” or aluminum lung among men engaged in the manufacturing of aluminum pyrotechnic flake powder used for explosives. The pyrotechnic flake powder is produced by crushing, grinding, and stamping aluminum. During stamping, the flake is lubricated with stearine, which forms a fine film of aluminum stearate on the surface of the particles and retards surface oxidation. The initial cases of aluminum lung were attributed to the absence of stearine in the process because of war-time shortage3; however, other reports have shown that pulmonary fibrosis can occur in the workers even when the flake is lubricated with stearine.4 Aluminosis has since been reported in aluminum polishers,5 workers exposed to aluminum powder in aluminum powder mills,6 and aluminum welders exposed to aerosols of oxidized aluminum.7,8 There are also case reports of aluminosis presenting predominantly with mediastinal lymphadenopathy, with evidence of aluminum particles in the mediastinal lymph nodes.9,10 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4131931/

  1. Goralewski G, Jaeger R. Clinical study, pathology and pathogenesis of the aluminum lung. Arch Gewebepathol Gewerbehygiene. 1941;11:102–105

Maybe synonym of pulmonary aluminosis. Need to investigate more

nicolevasilevsky commented 6 years ago

@GARDInfoCenter I added this def for aluminum lung, let me know if you'd like any revisions. Would you like the synonym 'pulmonary aluminosis' too?

Def: Aluminium lung is characterized as diffuse interstitial fibrosis which is mainly located in the upper and middle lobes of the lung. In advanced stages it is characterized by subpleural bullous emphysema with an increased risk of spontaneous pneumothorax. PMID:16722569

cmungall commented 6 years ago

Remember we default to US spelling (but have UK as synonym)

@nicolevasilevsky - we have this pattern for environmental disease: https://github.com/monarch-initiative/mondo-build/blob/master/src/patterns/environmental_stimulus.yaml

can can you request a dust term here: https://github.com/EnvironmentOntology/envo/issues/583

nicolevasilevsky commented 6 years ago

I fixed the spelling and added the synonym

nicolevasilevsky commented 6 years ago

@GARDInfoCenter should we add the synonym aluminiumlunge as well?

GARDInfoCenter commented 6 years ago

@nicolevasilevsky for historical purposes, I would recommend you add aluminiumlunge as a synonym.

We are in contact with several groups about adding "pulmonary aluminosis" as a synonym and the definition you have developed. Hope to get back to you later today.

GARDInfoCenter commented 6 years ago

We don't delete terms/diseases from our list; we simply retire them. Below is a synopsis of what we found and what action we took for the list of diseases.

• alopecia immunodeficiency (retired) o Retired because it is a duplicated term for alymphoid cystic thymic dysgenesis. Unable to find any articles in Pubmed or other sites.

• alpha-2 deficient collagen disease (retired) o Retired because this term was based in a single report in 1979 about a boy who could have another diagnosis: Meigel, W. N., Muller, P. K., Pontz, B. F., Sorensen, N., Spranger, J. W. A constitutional disorder of connective tissue suggesting a defect in collagen biosynthesis. Klin. Wschr. 52: 906-912, 1974

• aluminium lung (got a call into several groups waiting to hear back regarding whether “pulmonary aluminosis” is a synonym and whether the proposed description/definition is fine)

• amelia cleft lip palate hydrocephalus iris coloboma (OMIM 601357) o Pubmed articles:  https://www.ncbi.nlm.nih.gov/pubmed/7981864https://www.ncbi.nlm.nih.gov/pubmed/19938097https://www.ncbi.nlm.nih.gov/pubmed/10748410

• ankle defects short stature (retired) o Did not find any information for this condition.

• Apert-like polydactyly syndrome (retired) o Did not find any information for this condition.

cmungall commented 6 years ago

Thanks! Are the retired terms still available via the GARD API?

On 12 Mar 2018, at 9:16, GARDInfoCenter wrote:

We don't delete terms/diseases from our list; we simply retire them. Below is a synopsis of what we found and what action we took for the list of diseases.

• alopecia immunodeficiency (retired) o Retired because it is a duplicated term for alymphoid cystic thymic dysgenesis. Unable to find any articles in Pubmed or other sites.

• alpha-2 deficient collagen disease (retired) o Retired because this term was based in a single report in 1979 about a boy who could have another diagnosis: Meigel, W. N., Muller, P. K., Pontz, B. F., Sorensen, N., Spranger, J. W. A constitutional disorder of connective tissue suggesting a defect in collagen biosynthesis. Klin. Wschr. 52: 906-912, 1974

• aluminium lung (got a call into several groups waiting to hear back regarding whether “pulmonary aluminosis” is a synonym and whether the proposed description/definition is fine)

• amelia cleft lip palate hydrocephalus iris coloboma (OMIM 601357) o Pubmed articles:  https://www.ncbi.nlm.nih.gov/pubmed/7981864https://www.ncbi.nlm.nih.gov/pubmed/19938097https://www.ncbi.nlm.nih.gov/pubmed/10748410

• ankle defects short stature (retired) o Did not find any information for this condition.

• Apert-like polydactyly syndrome (retired) o Did not find any information for this condition.

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/monarch-initiative/mondo-build/issues/79#issuecomment-372368327

nicolevasilevsky commented 6 years ago
GARDInfoCenter commented 6 years ago

After speaking w/ several sources at the CDC, NHLBI, and NIAID, we have decided that we will replace the term "aluminum lung" with the term aluminosis (synonyms: aluminosis of lung; pulmonary aluminosis). The term "aluminum lung" is not a widely recognized disease and appears to have only been used in the 1941 article referenced above.

nicolevasilevsky commented 6 years ago

@GARDInfoCenter sounds good, I'll make that change asap.

nicolevasilevsky commented 6 years ago

@cmungall I am getting crazy diffs again when I try to edit MONDO

nicolevasilevsky commented 3 years ago

What is needed:

  1. do SPARQL query for missing defs for GARD terms
  2. write definitions
nicolevasilevsky commented 3 years ago

@matentzn - could you help do the SPARQL query above (do SPARQL query for missing defs for GARD terms) and then @kallia-p could you work on adding definitions for terms that are missing definitions. There may be some definitions on the GARD website: https://rarediseases.info.nih.gov/about-gard/pages/23/about-gard

If there is not a definition on the GARD site, you'll need to find a paper on PubMed that describes the disease.

Thank you!

matentzn commented 3 years ago

Coole. Added a table is here.

Query is this one:

prefix owl: <http://www.w3.org/2002/07/owl#>
prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT distinct ?term ?term_label ?xref
WHERE 
{ 
    ?term rdfs:label ?term_label ;
      oboInOwl:hasDbXref ?xref ;
      a owl:Class .
        [ a owl:Axiom ;
           owl:annotatedSource ?term ;
           owl:annotatedProperty oboInOwl:hasDbXref ;
           owl:annotatedTarget ?xref ;
           oboInOwl:source ?source 
        ] .
    FILTER NOT EXISTS {
        ?term <http://purl.obolibrary.org/obo/IAO_0000115> ?def .
    }
    FILTER (STRSTARTS(str(?xref),"GARD"))
    FILTER (str(?source)="MONDO:equivalentTo")
    FILTER (isIRI(?term) && regex(str(?term), "^http://purl.obolibrary.org/obo/MONDO_"))
}

@kallia-p check 1 or 2 manually of these just to be certain I didn't make a mistake.

kallia-p commented 3 years ago

@nicolevasilevsky @matentzn Checked the first couple of terms in OLS and there is no definition for them

nicolevasilevsky commented 3 years ago

@matentzn - this looks perfect, thanks for doing this so quickly!

Hi @kallia-p yes, that's correct. These terms do not have definitions and the task is to add definitions. It seems that there are a lot of terms in this spreadsheet (over 1,000), so this will be a big project. I recommend working on this a little bit each week.

I checked the first few terms and there are not definitions in GARD. I recommend that you search for these disease names in PubMed and see if you can find a paper that discusses these diseases and write a definition for each term and add it in Protege.

Before you get started, please see Chris' blog about writing good text definitions: https://douroucouli.wordpress.com/2019/07/08/ontotip-write-simple-concise-clear-operational-textual-definitions/

Let me know if you have further questions, thank you!

kallia-p commented 3 years ago

@nicolevasilevsky I am looking to add missing definitions and I was wondering do we have a pattern for contiguous gene diseases? The term that I am looking at is chondrodysplasia punctata with steroid sulfatase deficiency MONDO:0022729. In MONDO we have chondrodysplasia punctata MONDO:0019701 defined as 'A rare congenital developmental disorder characterized by the presence of stippled foci of calcification in the hyaline cartilage, joint contractions, mental retardation and ichthyosis.' In MONDO we also have the term 'recessive X-linked ichthyosis' defined as 'Recessive X-linked ichthyosis (RXLI) is a genodermatosis belonging to the Mendelian Disorders of Cornification (MeDOC) and characterized by generalized hyperkeratosis and scaling of the skin'. This term has an OMIM dbxref https://omim.org/entry/308100 ICHTHYOSIS, X-LINKED; XLI and alternative title STEROID SULFATASE DEFICIENCY. The OMIM entry includes the entity ICHTHYOSIS, X-LINKED, COMPLICATED, INCLUDED which describes the contiguous gene syndrome. Ballabio 1989 et al., PubMed:3165728. Short stature, chondrodysplasia punctata, mental retardation, steroid sulfatase deficiency, and Kallmann syndrome have been found as isolated entities or associated in various combinations in 27 patients with interstitial and terminal deletions involving the distal short arm of the X chromosome. One patient with X-linked ichthyosis and X-linked chondrodysplasia punctata PubMed: 3165728 has the karyotype 46,Y,der(X),t(X;Y)(p22.3;qll)

So the definition could be A rare congenital developmental disorder characterized by the presence of stippled foci of calcification in the hyaline cartilage, joint contractions, mental retardation and ichthyosis due to steroid sulfatase deficiency.

Then we will need to add chondrodysplasia punctata as a parent class.

nicolevasilevsky commented 3 years ago

Hi @kallia-p I don't believe we have a pattern for contiguous gene diseases.

Yes, I agree chondrodysplasia punctata should be a parent class.

You don't need to repeat the definition of the parent class, the definition could be: Any chondrodysplasia punctata where there is a deficiency in steroid sulfatase, an enzyme responsible for the hydrolysis of aryl and alkyl steroid sulfates and therefore has a pivotal role in regulating the formation of biologically active steroids. dbxref: PMID:15561802

kallia-p commented 3 years ago

@nicolevasilevsky Thanks for your input.

nicolevasilevsky commented 2 years ago

This ticket is too large. We discussed on the curation call, okay to close.