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Jun 20, 2023
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Issues around canonical ordering #285

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b823f7f
Update mp-hp-exact-0.0.1.sssom.tsv
matentzn Jun 11, 2023
7e6cba5
Apply sort order to all example files
matentzn Jun 11, 2023
227366c
Fix a bit of wording in the SPEC
matentzn Jun 11, 2023
fe9748c
Update CHANGELOG.md
matentzn Jun 11, 2023
a97037c
Update spec.md
matentzn Jun 11, 2023
7596aa8
Update src/docs/spec.md
matentzn Jun 11, 2023
d2e4075
Update semapv namespace
matentzn Jun 11, 2023
73ec4c8
Merge branch 'change-col-order-example' of https://github.com/mapping…
matentzn Jun 11, 2023
74425e9
minor change to trigger workflow.
hrshdhgd Jun 19, 2023
b01362d
Added `vocab/` to `semapv` URI
hrshdhgd Jun 19, 2023
1d5606b
Merge branch 'master' into change-col-order-example
hrshdhgd Jun 19, 2023
d2016bc
ran make all again
hrshdhgd Jun 19, 2023
348e442
reverted pminor changes previously made
hrshdhgd Jun 19, 2023
8874671
Update CHANGELOG.md
matentzn Jun 20, 2023
786b877
Merge branch 'master' into change-col-order-example
matentzn Jun 20, 2023
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2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/new_sssom_element.md
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Expand Up @@ -34,7 +34,7 @@ Example description.
# owl: http://www.w3.org/2002/07/owl#
# rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
# rdfs: http://www.w3.org/2000/01/rdf-schema#
# semapv: https://w3id.org/semapv/
# semapv: https://w3id.org/semapv/vocab/
# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://w3id.org/sssom/license/unspecified
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5 changes: 3 additions & 2 deletions CHANGELOG.md
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@@ -1,8 +1,9 @@
# Changelog for SSSOM

## SSSOM version 1.0
## SSSOM version 0.13.0

- TBD
- The necessity of the "canonical column ordering" was downgraded from MUST to SHOULD (https://github.com/mapping-commons/sssom/pull/285)
- Documents clearly that built-in prefixes MUST NOT be redefined (https://github.com/mapping-commons/sssom/pull/285)

## SSSOM version 0.11.0

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13 changes: 9 additions & 4 deletions examples/embedded/foodie-inc-2022-05-01.sssom.tsv
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# comment: We could map to FOODON:00004187 instead which more specifically refers to
# 'raw' Pink apples. Decided against to be consistent with other mapping choices.
# curie_map:
# FOODON: http://purl.obolibrary.org/obo/FOODON_
# KF_FOOD: https://kewl-foodie.inc/food/
# orcid: https://orcid.org/
# owl: http://www.w3.org/2002/07/owl#
# rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
# rdfs: http://www.w3.org/2000/01/rdf-schema#
# semapv: https://w3id.org/semapv/vocab/
# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# orcid: https://orcid.org/
# wikidata: https://www.wikidata.org/wiki/
# mapping_set_id: https://w3id.org/sssom/tutorial/example1.sssom.tsv
# license: https://creativecommons.org/licenses/by/4.0/
# mapping_date: '2022-05-02'
# mapping_set_description: Manually curated alignment of KEWL FOODIE INC internal food
# and nutrition database with Food Ontology (FOODON). Intended to be used for ontological
# analysis and grouping of KEWL FOODIE INC related data.
# mapping_set_id: https://w3id.org/sssom/tutorial/example1.sssom.tsv
# mapping_set_version: '2022-05-01'
# object_source: wikidata:Q55118395
# object_source_version: http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl
# subject_source: KF_FOOD:DB
# comment: We could map to FOODON:00004187 instead which more specifically refers to
# 'raw' Pink apples. Decided against to be consistent with other mapping choices.
subject_id subject_label predicate_id object_id object_label mapping_justification author_id object_source_version mapping_date confidence comment
KF_FOOD:F001 apple skos:exactMatch FOODON:00002473 apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 0.95 "We could map to FOODON:03310788 instead to cover sliced apples, but only ""whole"" apple types exist."
KF_FOOD:F002 gala skos:exactMatch FOODON:00003348 Gala apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0
KF_FOOD:F003 pink skos:exactMatch FOODON:00004187 Pink apple (whole, raw) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 0.9 "We could map to FOODON:00004187 instead which more specifically refers to ""raw"" Pink apples. Decided against to be consistent with other mapping choices."
KF_FOOD:F004 braeburn skos:exactMatch sssom:NoMapping semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0
KF_FOOD:F004 braeburn skos:broadMatch FOODON:00002473 apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0

104 changes: 56 additions & 48 deletions examples/embedded/mp-hp-exact-0.0.1.sssom.tsv
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#curie_map:
# HP: "http://purl.obolibrary.org/obo/HP_"
# MP: "http://purl.obolibrary.org/obo/MP_"
#license: "https://creativecommons.org/publicdomain/zero/1.0/"
#mapping_provider: "http://purl.obolibrary.org/obo/upheno.owl"
subject_id predicate_id object_id mapping_justification subject_label object_label
HP:0009124 skos:exactMatch MP:0000003 semapv:LexicalMatching Abnormal adipose tissue morphology abnormal adipose tissue morphology
HP:0008551 skos:exactMatch MP:0000018 semapv:LexicalMatching Microtia small ears
HP:0000411 skos:exactMatch MP:0000021 semapv:LexicalMatching Protruding ear prominent ears
HP:0000375 skos:exactMatch MP:0000031 semapv:LexicalMatching Abnormal cochlea morphology abnormal cochlea morphology
HP:0009910 skos:exactMatch MP:0000040 semapv:LexicalMatching Aplasia of the middle ear ossicles absent middle ear ossicles
HP:0002659 skos:exactMatch MP:0000061 semapv:LexicalMatching Increased susceptibility to fractures fragile skeleton
HP:0004349 skos:exactMatch MP:0000063 semapv:LexicalMatching Reduced bone mineral density decreased bone mineral density
HP:0011002 skos:exactMatch MP:0000067 semapv:LexicalMatching Osteopetrosis osteopetrosis
HP:0001363 skos:exactMatch MP:0000081 semapv:LexicalMatching Craniosynostosis premature cranial suture closure
HP:0000260 skos:exactMatch MP:0000085 semapv:LexicalMatching Wide anterior fontanel large anterior fontanelle
HP:0009939 skos:exactMatch MP:0000087 semapv:LexicalMatching Mandibular aplasia absent mandible
HP:0100629 skos:exactMatch MP:0000108 semapv:LexicalMatching Midline facial cleft midline facial cleft
HP:0000175 skos:exactMatch MP:0000111 semapv:LexicalMatching Cleft palate cleft palate
HP:0400001 skos:exactMatch MP:0000114 semapv:LexicalMatching Chin with vertical crease cleft chin
HP:0006288 skos:exactMatch MP:0000122 semapv:LexicalMatching Advanced eruption of teeth premature tooth eruption
HP:0100671 skos:exactMatch MP:0000130 semapv:LexicalMatching Abnormal trabecular bone morphology abnormal trabecular bone morphology
HP:0003307 skos:exactMatch MP:0000162 semapv:LexicalMatching Hyperlordosis lordosis
HP:0002763 skos:exactMatch MP:0000163 semapv:LexicalMatching Abnormal cartilage morphology abnormal cartilage morphology
HP:0031851 skos:exactMatch MP:0000208 semapv:LexicalMatching Reduced hematocrit decreased hematocrit
HP:0001974 skos:exactMatch MP:0000218 semapv:LexicalMatching Leukocytosis increased leukocyte cell number
HP:0011897 skos:exactMatch MP:0000219 semapv:LexicalMatching Neutrophilia increased neutrophil cell number
HP:0001882 skos:exactMatch MP:0000221 semapv:LexicalMatching Leukopenia decreased leukocyte cell number
HP:0025065 skos:exactMatch MP:0000226 semapv:LexicalMatching Abnormal mean corpuscular volume abnormal mean corpuscular volume
HP:0000822 skos:exactMatch MP:0000231 semapv:LexicalMatching Hypertension hypertension
HP:0001978 skos:exactMatch MP:0000240 semapv:LexicalMatching Extramedullary hematopoiesis extramedullary hematopoiesis
HP:0001336 skos:exactMatch MP:0000243 semapv:LexicalMatching Myoclonus myoclonus
HP:0001627 skos:exactMatch MP:0000266 semapv:LexicalMatching Abnormal heart morphology abnormal heart morphology
HP:0001679 skos:exactMatch MP:0000272 semapv:LexicalMatching Abnormal aortic morphology abnormal aorta morphology
HP:0001667 skos:exactMatch MP:0000276 semapv:LexicalMatching Right ventricular hypertrophy heart right ventricle hypertrophy
HP:0001719 skos:exactMatch MP:0000284 semapv:LexicalMatching Double outlet right ventricle double outlet right ventricle
HP:0001633 skos:exactMatch MP:0000286 semapv:LexicalMatching Abnormal mitral valve morphology abnormal mitral valve morphology
HP:0001981 skos:exactMatch MP:0000314 semapv:LexicalMatching Schistocytosis schistocytosis
HP:0032310 skos:exactMatch MP:0000322 semapv:LexicalMatching Granulocytosis increased granulocyte number
HP:0012543 skos:exactMatch MP:0000327 semapv:LexicalMatching Hemosiderinuria hemosiderinuria
HP:0001913 skos:exactMatch MP:0000334 semapv:LexicalMatching Granulocytopenia decreased granulocyte number
HP:0012234 skos:exactMatch MP:0000334 semapv:LexicalMatching Agranulocytosis decreased granulocyte number
HP:0031377 skos:exactMatch MP:0000350 semapv:LexicalMatching Abnormal cell proliferation abnormal cell proliferation
HP:0025084 skos:exactMatch MP:0000376 semapv:LexicalMatching Folliculitis folliculitis
HP:0002212 skos:exactMatch MP:0000410 semapv:LexicalMatching Curly hair waved hair
HP:0001596 skos:exactMatch MP:0000414 semapv:LexicalMatching Alopecia alopecia
HP:0011457 skos:exactMatch MP:0000425 semapv:LexicalMatching Loss of eyelashes loss of eyelid cilia
HP:0000252 skos:exactMatch MP:0000433 semapv:LexicalMatching Microcephaly microcephaly
# curie_map:
# HP: http://purl.obolibrary.org/obo/HP_
# MP: http://purl.obolibrary.org/obo/MP_
# owl: http://www.w3.org/2002/07/owl#
# rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
# rdfs: http://www.w3.org/2000/01/rdf-schema#
# semapv: https://w3id.org/semapv/vocab/
# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://creativecommons.org/publicdomain/zero/1.0/
# mapping_provider: http://purl.obolibrary.org/obo/upheno.owl
# mapping_set_id: https://w3id.org/sssom/mappings/27f85fe9-8a72-4e76-909b-7ba4244d9ede
subject_id subject_label predicate_id object_id object_label mapping_justification
HP:0000175 Cleft palate skos:exactMatch MP:0000111 cleft palate semapv:LexicalMatching
HP:0000252 Microcephaly skos:exactMatch MP:0000433 microcephaly semapv:LexicalMatching
HP:0000260 Wide anterior fontanel skos:exactMatch MP:0000085 large anterior fontanelle semapv:LexicalMatching
HP:0000375 Abnormal cochlea morphology skos:exactMatch MP:0000031 abnormal cochlea morphology semapv:LexicalMatching
HP:0000411 Protruding ear skos:exactMatch MP:0000021 prominent ears semapv:LexicalMatching
HP:0000822 Hypertension skos:exactMatch MP:0000231 hypertension semapv:LexicalMatching
HP:0001336 Myoclonus skos:exactMatch MP:0000243 myoclonus semapv:LexicalMatching
HP:0001363 Craniosynostosis skos:exactMatch MP:0000081 premature cranial suture closure semapv:LexicalMatching
HP:0001596 Alopecia skos:exactMatch MP:0000414 alopecia semapv:LexicalMatching
HP:0001627 Abnormal heart morphology skos:exactMatch MP:0000266 abnormal heart morphology semapv:LexicalMatching
HP:0001633 Abnormal mitral valve morphology skos:exactMatch MP:0000286 abnormal mitral valve morphology semapv:LexicalMatching
HP:0001667 Right ventricular hypertrophy skos:exactMatch MP:0000276 heart right ventricle hypertrophy semapv:LexicalMatching
HP:0001679 Abnormal aortic morphology skos:exactMatch MP:0000272 abnormal aorta morphology semapv:LexicalMatching
HP:0001719 Double outlet right ventricle skos:exactMatch MP:0000284 double outlet right ventricle semapv:LexicalMatching
HP:0001882 Leukopenia skos:exactMatch MP:0000221 decreased leukocyte cell number semapv:LexicalMatching
HP:0001913 Granulocytopenia skos:exactMatch MP:0000334 decreased granulocyte number semapv:LexicalMatching
HP:0001974 Leukocytosis skos:exactMatch MP:0000218 increased leukocyte cell number semapv:LexicalMatching
HP:0001978 Extramedullary hematopoiesis skos:exactMatch MP:0000240 extramedullary hematopoiesis semapv:LexicalMatching
HP:0001981 Schistocytosis skos:exactMatch MP:0000314 schistocytosis semapv:LexicalMatching
HP:0002212 Curly hair skos:exactMatch MP:0000410 waved hair semapv:LexicalMatching
HP:0002659 Increased susceptibility to fractures skos:exactMatch MP:0000061 fragile skeleton semapv:LexicalMatching
HP:0002763 Abnormal cartilage morphology skos:exactMatch MP:0000163 abnormal cartilage morphology semapv:LexicalMatching
HP:0003307 Hyperlordosis skos:exactMatch MP:0000162 lordosis semapv:LexicalMatching
HP:0004349 Reduced bone mineral density skos:exactMatch MP:0000063 decreased bone mineral density semapv:LexicalMatching
HP:0006288 Advanced eruption of teeth skos:exactMatch MP:0000122 premature tooth eruption semapv:LexicalMatching
HP:0008551 Microtia skos:exactMatch MP:0000018 small ears semapv:LexicalMatching
HP:0009124 Abnormal adipose tissue morphology skos:exactMatch MP:0000003 abnormal adipose tissue morphology semapv:LexicalMatching
HP:0009910 Aplasia of the middle ear ossicles skos:exactMatch MP:0000040 absent middle ear ossicles semapv:LexicalMatching
HP:0009939 Mandibular aplasia skos:exactMatch MP:0000087 absent mandible semapv:LexicalMatching
HP:0011002 Osteopetrosis skos:exactMatch MP:0000067 osteopetrosis semapv:LexicalMatching
HP:0011457 Loss of eyelashes skos:exactMatch MP:0000425 loss of eyelid cilia semapv:LexicalMatching
HP:0011897 Neutrophilia skos:exactMatch MP:0000219 increased neutrophil cell number semapv:LexicalMatching
HP:0012234 Agranulocytosis skos:exactMatch MP:0000334 decreased granulocyte number semapv:LexicalMatching
HP:0012543 Hemosiderinuria skos:exactMatch MP:0000327 hemosiderinuria semapv:LexicalMatching
HP:0025065 Abnormal mean corpuscular volume skos:exactMatch MP:0000226 abnormal mean corpuscular volume semapv:LexicalMatching
HP:0025084 Folliculitis skos:exactMatch MP:0000376 folliculitis semapv:LexicalMatching
HP:0031377 Abnormal cell proliferation skos:exactMatch MP:0000350 abnormal cell proliferation semapv:LexicalMatching
HP:0031851 Reduced hematocrit skos:exactMatch MP:0000208 decreased hematocrit semapv:LexicalMatching
HP:0032310 Granulocytosis skos:exactMatch MP:0000322 increased granulocyte number semapv:LexicalMatching
HP:0100629 Midline facial cleft skos:exactMatch MP:0000108 midline facial cleft semapv:LexicalMatching
HP:0100671 Abnormal trabecular bone morphology skos:exactMatch MP:0000130 abnormal trabecular bone morphology semapv:LexicalMatching
HP:0400001 Chin with vertical crease skos:exactMatch MP:0000114 cleft chin semapv:LexicalMatching

12 changes: 6 additions & 6 deletions examples/external/example1.sssom.tsv
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subject_id subject_label predicate_id object_id object_label confidence comment mapping_justification mapping_date author_id subject_source_version object_source_version
KF_FOOD:F001 apple skos:exactMatch FOODON:00002473 apple (whole) 0.95 We could map to FOODON:03310788 instead to cover sliced apples, but only "whole" apple types exist. semapv:ManualMappingCuration 2022-05-02 orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl
KF_FOOD:F002 gala skos:exactMatch FOODON:00003348 Gala apple (whole) 1 semapv:ManualMappingCuration 2022-05-02 orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl
KF_FOOD:F003 pink skos:exactMatch FOODON:00004186 Pink apple (whole) 0.9 We could map to FOODON:00004187 instead which more specifically refers to "raw" Pink apples. Decided against to be consistent with other mapping choices. semapv:ManualMappingCuration 2022-05-02 orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl
KF_FOOD:F004 braeburn skos:exactMatch sssom:NoMapping 1 semapv:ManualMappingCuration 2022-05-02 orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl
KF_FOOD:F004 braeburn skos:broadMatch FOODON:00002473 apple (whole) 1 semapv:ManualMappingCuration 2022-05-02 orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl
subject_id subject_label predicate_id object_id object_label mapping_justification author_id object_source_version mapping_date confidence comment
KF_FOOD:F001 apple skos:exactMatch FOODON:00002473 apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 0.95 "We could map to FOODON:03310788 instead to cover sliced apples, but only ""whole"" apple types exist."
KF_FOOD:F002 gala skos:exactMatch FOODON:00003348 Gala apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0
KF_FOOD:F003 pink skos:exactMatch FOODON:00004187 Pink apple (whole, raw) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 0.9 "We could map to FOODON:00004187 instead which more specifically refers to ""raw"" Pink apples. Decided against to be consistent with other mapping choices."
KF_FOOD:F004 braeburn skos:exactMatch sssom:NoMapping semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0
KF_FOOD:F004 braeburn skos:broadMatch FOODON:00002473 apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0
32 changes: 21 additions & 11 deletions examples/external/example1.sssom.yml
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mapping_set_id: https://w3id.org/sssom/tutorial/example1.sssom.tsv
license: https://creativecommons.org/licenses/by/4.0/
mapping_set_version: "2022-06-01"
mapping_set_description: "Manually curated alignment of KEWL FOODIE INC internal food and nutrition database with Food Ontology (FOODON). Intended to be used for ontological analysis and grouping of KEWL FOODIE INC related data."
object_source: wikidata:Q55118395
subject_source: KF_FOOD:DB
comment: We could map to FOODON:00004187 instead which more specifically refers to
'raw' Pink apples. Decided against to be consistent with other mapping choices.
curie_map:
KF_FOOD: https://kewl-foodie.inc/food/
wikidata: http://www.wikidata.org/entity/
FOODON: http://purl.obolibrary.org/obo/FOODON_
sempav: https://w3id.org/semapv/
skos: "http://www.w3.org/2004/02/skos/core#"
sssom: https://w3id.org/sssom/
KF_FOOD: https://kewl-foodie.inc/food/
orcid: https://orcid.org/
owl: http://www.w3.org/2002/07/owl#
rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs: http://www.w3.org/2000/01/rdf-schema#
semapv: https://w3id.org/semapv/vocab/
skos: http://www.w3.org/2004/02/skos/core#
sssom: https://w3id.org/sssom/
wikidata: https://www.wikidata.org/wiki/
license: https://creativecommons.org/licenses/by/4.0/
mapping_date: '2022-05-02'
mapping_set_description: Manually curated alignment of KEWL FOODIE INC internal food
and nutrition database with Food Ontology (FOODON). Intended to be used for ontological
analysis and grouping of KEWL FOODIE INC related data.
mapping_set_id: https://w3id.org/sssom/tutorial/example1.sssom.tsv
mapping_set_version: '2022-05-01'
object_source: wikidata:Q55118395
object_source_version: http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl
subject_source: KF_FOOD:DB
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