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Refresh imports for Uberon release (#3461)
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* Refresh imports for Uberon release

* Remove UBERON_0011940 from the HRA subset

This term was wrongly added into HRA (human don't have whiskers) and it needs to be removed from the ASCT+B tables
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@aleixpuigb
aleixpuigb authored Jan 14, 2025
1 parent ec4fed2 commit 41c24df
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Showing 11 changed files with 8,051 additions and 3,948 deletions.
40 changes: 19 additions & 21 deletions src/mappings/biomappings.sssom.tsv
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#curie_map:
# BTO: "http://purl.obolibrary.org/obo/BTO_"
# IDOMAL: "http://purl.obolibrary.org/obo/IDOMAL_"
# UBERON: "http://purl.obolibrary.org/obo/UBERON_"
# VO: "http://purl.obolibrary.org/obo/VO_"
# mesh: "http://id.nlm.nih.gov/mesh/"
# obo: "http://purl.obolibrary.org/obo/"
# orcid: "https://orcid.org/"
#mapping_set_id: "https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv"
#mapping_set_version: "0.3.8.dev0"
#mapping_set_title: "Biomappings"
#mapping_set_description: "Biomappings is a repository of community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources. It's also a place where anyone can contribute curations of predicted mappings or their own novel mappings."
# BTO: http://purl.obolibrary.org/obo/BTO_
# IDOMAL: http://purl.obolibrary.org/obo/IDOMAL_
# UBERON: http://purl.obolibrary.org/obo/UBERON_
# VO: http://purl.obolibrary.org/obo/VO_
# mesh: http://id.nlm.nih.gov/mesh/
# orcid: https://orcid.org/
#mapping_set_id: https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv
#mapping_set_version: 0.3.8.dev0
#mapping_set_title: Biomappings
#mapping_set_description: Biomappings is a repository of community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources. It's also a place where anyone can contribute curations of predicted mappings or their own novel mappings.
#creator_id:
# - "orcid:0000-0001-9439-5346"
# - "orcid:0000-0002-1216-4761"
# - "orcid:0000-0002-2046-6145"
# - "orcid:0000-0002-2627-0696"
# - "orcid:0000-0002-6601-2165"
# - "orcid:0000-0003-1307-2508"
# - "orcid:0000-0003-4423-4370"
#license: "https://creativecommons.org/publicdomain/zero/1.0/"
#subject_source: "obo:uberon/core.owl"
#mapping_provider: "https://github.com/biopragmatics/biomappings"
# - orcid:0000-0001-9439-5346
# - orcid:0000-0002-1216-4761
# - orcid:0000-0002-2046-6145
# - orcid:0000-0002-2627-0696
# - orcid:0000-0002-6601-2165
# - orcid:0000-0003-1307-2508
# - orcid:0000-0003-4423-4370
#license: https://creativecommons.org/publicdomain/zero/1.0/
#mapping_provider: https://github.com/biopragmatics/biomappings
subject_id subject_label predicate_id predicate_modifier object_id object_label mapping_justification author_id mapping_tool confidence
UBERON:0000016 endocrine pancreas skos:exactMatch mesh:D007515 Islets of Langerhans semapv:LexicalMatching generate_uberon_mesh_mappings.py 0.9
UBERON:0000017 exocrine pancreas skos:exactMatch mesh:D046790 Pancreas, Exocrine semapv:ManualMappingCuration orcid:0000-0001-9439-5346
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2,855 changes: 1,421 additions & 1,434 deletions src/mappings/cl.sssom.tsv
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24 changes: 12 additions & 12 deletions src/mappings/fbbt.sssom.tsv
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#curie_map:
# FBbt: "http://purl.obolibrary.org/obo/FBbt_"
# ORCID: "https://orcid.org/"
# UBERON: "http://purl.obolibrary.org/obo/UBERON_"
# obo: "http://purl.obolibrary.org/obo/"
#mapping_set_id: "http://purl.obolibrary.org/obo/fbbt/fbbt-mappings.sssom.tsv"
#mapping_set_description: "Mappings between the Drosophila Anatomy Ontology and foreign ontologies."
# FBbt: http://purl.obolibrary.org/obo/FBbt_
# ORCID: https://orcid.org/
# UBERON: http://purl.obolibrary.org/obo/UBERON_
# obo: http://purl.obolibrary.org/obo/
#mapping_set_id: http://purl.obolibrary.org/obo/fbbt/fbbt-mappings.sssom.tsv
#mapping_set_description: Mappings between the Drosophila Anatomy Ontology and foreign ontologies.
#creator_id:
# - "ORCID:0000-0002-1373-1705"
# - "ORCID:0000-0002-6095-8718"
#license: "https://creativecommons.org/licenses/by/4.0/"
#subject_source: "obo:fbbt.owl"
#object_source: "obo:uberon/core.owl"
#mapping_date: "2024-07-12"
# - ORCID:0000-0002-1373-1705
# - ORCID:0000-0002-6095-8718
#license: https://creativecommons.org/licenses/by/4.0/
#subject_source: obo:fbbt.owl
#object_source: obo:uberon.owl
#mapping_date: 2024-07-12
subject_id subject_label predicate_id object_id object_label mapping_justification comment
FBbt:00000001 organism semapv:crossSpeciesExactMatch UBERON:0000468 multicellular organism semapv:ManualMappingCuration
FBbt:00000002 tagma semapv:crossSpeciesExactMatch UBERON:6000002 arthropod tagma semapv:ManualMappingCuration
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36 changes: 18 additions & 18 deletions src/ontology/components/hra_subset.owl
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<!-- http://purl.obolibrary.org/obo/UBERON_0002033 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0002033">
<obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/UBERON_0002037 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0002037">
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<!-- http://purl.obolibrary.org/obo/UBERON_0005975 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0005975">
<obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/UBERON_0006082 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0006082">
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<!-- http://purl.obolibrary.org/obo/UBERON_0006763 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0006763">
<obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/UBERON_0006764 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0006764">
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<!-- http://purl.obolibrary.org/obo/UBERON_0009967 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0009967">
<obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/UBERON_0009980 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0009980">
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