Skip to content

Update all registry files #32

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
matentzn merged 1 commit into from
Oct 15, 2026
Merged

Update all registry files #32

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
123 changes: 68 additions & 55 deletions data/mapping-specifications.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -246,7 +246,7 @@
},
{
"id": "http://purl.obolibrary.org/obo/mondo/mappings/mondo_hasdbxref_icd10cm.sssom.tsv",
"version": "http://purl.obolibrary.org/obo/mondo/releases/2026-09-01/mappings/mondo_hasdbxref_icd10cm.sssom.tsv",
"version": "http://purl.obolibrary.org/obo/mondo/releases/2026-10-06/mappings/mondo_hasdbxref_icd10cm.sssom.tsv",
"license": "https://creativecommons.org/publicdomain/zero/1.0/",
"type": "sssom",
"subject_source": {
Expand Down Expand Up @@ -284,7 +284,7 @@
"id": "https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv",
"name": "Biomappings",
"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.",
"version": "0.6.1-dev-5d3d419d",
"version": "0.6.1-dev-ed12b9f4",
"license": "https://creativecommons.org/publicdomain/zero/1.0/",
"type": "sssom",
"content_url": "http://w3id.org/sssom/commons/monarch/mappings/mesh_chebi_biomappings.sssom.tsv",
Expand Down Expand Up @@ -440,7 +440,7 @@
},
{
"id": "http://purl.obolibrary.org/obo/mondo/mappings/mondo_hasdbxref_hp.sssom.tsv",
"version": "http://purl.obolibrary.org/obo/mondo/releases/2026-09-01/mappings/mondo_hasdbxref_hp.sssom.tsv",
"version": "http://purl.obolibrary.org/obo/mondo/releases/2026-10-06/mappings/mondo_hasdbxref_hp.sssom.tsv",
"license": "https://creativecommons.org/publicdomain/zero/1.0/",
"type": "sssom",
"subject_source": {
Expand Down Expand Up @@ -480,31 +480,34 @@
},
{
"id": "http://w3id.org/sssom/commons/monarch/mappings/loinc2chebi_1.sssom.tsv",
"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loinc2chebi_1.sssom.tsv",
"license": "https://github.com/mapping-commons/mapping-commons.github.io/blob/main/docs/original_license_applies.md",
"type": "sssom",
"status": "fetch_error",
"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loinc2chebi_1.sssom.tsv",
"registries": [
{
"id": "https://w3id.org/sssom/commons/monarch",
"name": "Monarch Mapping Commons",
"url": "https://github.com/monarch-initiative/monarch-mapping-commons"
}
],
"metadata_completeness_score": 0.0
"status": "ok",
"metadata_completeness_score": 0.2727
},
{
"id": "http://w3id.org/sssom/commons/monarch/mappings/loinc2chebi_2.sssom.tsv",
"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loinc2chebi_2.sssom.tsv",
"description": "LOINC part to ChEBI mappings. Parts carrying a '^' qualifier denote a measurement context (timing, specimen order, posture, challenge protocol) applied to the same underlying entity; these are asserted as skos:broadMatch, since the LOINC part is narrower than the ontology concept. Unqualified parts use skos:exactMatch. The predicate revision on qualified parts was applied programmatically; the underlying subject-object mappings are the original manual curation.",
"license": "http://creativecommons.org/publicdomain/zero/1.0/",
"type": "sssom",
"status": "fetch_error",
"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loinc2chebi_2.sssom.tsv",
"registries": [
{
"id": "https://w3id.org/sssom/commons/monarch",
"name": "Monarch Mapping Commons",
"url": "https://github.com/monarch-initiative/monarch-mapping-commons"
}
],
"metadata_completeness_score": 0.0
"status": "ok",
"metadata_completeness_score": 0.3409
},
{
"id": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2cl.sssom.tsv",
Expand All @@ -524,31 +527,34 @@
},
{
"id": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2go.sssom.tsv",
"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2go.sssom.tsv",
"license": "http://creativecommons.org/publicdomain/zero/1.0/",
"type": "sssom",
"status": "fetch_error",
"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2go.sssom.tsv",
"registries": [
{
"id": "https://w3id.org/sssom/commons/monarch",
"name": "Monarch Mapping Commons",
"url": "https://github.com/monarch-initiative/monarch-mapping-commons"
}
],
"metadata_completeness_score": 0.0
"status": "ok",
"metadata_completeness_score": 0.2727
},
{
"id": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2ncbitaxon.sssom.tsv",
"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2ncbitaxon.sssom.tsv",
"description": "LOINC part to NCBI Taxon mappings. Parts carrying a '^' qualifier denote a measurement context (timing, specimen order, posture, challenge protocol) applied to the same underlying entity; these are asserted as skos:broadMatch, since the LOINC part is narrower than the ontology concept. Unqualified parts use skos:exactMatch. The predicate revision on qualified parts was applied programmatically; the underlying subject-object mappings are the original manual curation.",
"license": "http://creativecommons.org/publicdomain/zero/1.0/",
"type": "sssom",
"status": "fetch_error",
"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2ncbitaxon.sssom.tsv",
"registries": [
{
"id": "https://w3id.org/sssom/commons/monarch",
"name": "Monarch Mapping Commons",
"url": "https://github.com/monarch-initiative/monarch-mapping-commons"
}
],
"metadata_completeness_score": 0.0
"status": "ok",
"metadata_completeness_score": 0.3409
},
{
"id": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2ncit.sssom.tsv",
Expand All @@ -567,31 +573,35 @@
},
{
"id": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2pr.sssom.tsv",
"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2pr.sssom.tsv",
"description": "LOINC part to Protein Ontology mappings. Parts carrying a '^' qualifier denote a measurement context (timing, specimen order, posture, challenge protocol) applied to the same underlying entity; these are asserted as skos:broadMatch, since the LOINC part is narrower than the ontology concept. Unqualified parts use skos:exactMatch. The predicate revision on qualified parts was applied programmatically; the underlying subject-object mappings are the original manual curation.",
"license": "http://creativecommons.org/publicdomain/zero/1.0/",
"type": "sssom",
"status": "fetch_error",
"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2pr.sssom.tsv",
"registries": [
{
"id": "https://w3id.org/sssom/commons/monarch",
"name": "Monarch Mapping Commons",
"url": "https://github.com/monarch-initiative/monarch-mapping-commons"
}
],
"metadata_completeness_score": 0.0
"status": "ok",
"metadata_completeness_score": 0.3409
},
{
"id": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2uberon.sssom.tsv",
"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2uberon.sssom.tsv",
"description": "This mapping set contains mappings between LOINC parts and Uberon anatomical entities. The predicate revision on qualified parts was applied programmatically; the underlying subject-object mappings are the original manual curation.",
"license": "http://creativecommons.org/publicdomain/zero/1.0/",
"type": "sssom",
"status": "fetch_error",
"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2uberon.sssom.tsv",
"registries": [
{
"id": "https://w3id.org/sssom/commons/monarch",
"name": "Monarch Mapping Commons",
"url": "https://github.com/monarch-initiative/monarch-mapping-commons"
}
],
"metadata_completeness_score": 0.0
"status": "ok",
"metadata_completeness_score": 0.3409
},
{
"id": "cpath_obo_omop",
Expand Down Expand Up @@ -625,38 +635,6 @@
"status": "ok",
"metadata_completeness_score": 0.3409
},
{
"id": "fars_obo_omop",
"description": "C-Path generated mappings of OBO to OMOP terms: FARS COA",
"license": "https://creativecommons.org/licenses/by-nc/4.0/",
"type": "sssom",
"content_url": "https://w3id.org/cpont/mappings/fars_obo_omop.cpath.sssom.tsv",
"registries": [
{
"id": "https://w3id.org/cpont/mappings",
"name": "C-Path Mapping Commons",
"url": "https://gitlab.c-path.org/c-pathontology/mapping-commons"
}
],
"status": "ok",
"metadata_completeness_score": 0.3409
},
{
"id": "fars_obo_omop_invert",
"description": "Inversion of the C-Path generated OBO to OMOP mappings: FARS COA",
"license": "https://creativecommons.org/licenses/by-nc/4.0/",
"type": "sssom",
"content_url": "https://w3id.org/cpont/mappings/fars_obo_omop_invert.cpath.sssom.tsv",
"registries": [
{
"id": "https://w3id.org/cpont/mappings",
"name": "C-Path Mapping Commons",
"url": "https://gitlab.c-path.org/c-pathontology/mapping-commons"
}
],
"status": "ok",
"metadata_completeness_score": 0.3409
},
{
"id": "https://doi.org/10.5281/zenodo.7250177",
"version": "V1.5",
Expand Down Expand Up @@ -707,7 +685,7 @@
},
{
"id": "http://purl.obolibrary.org/obo/mondo/mappings/mondo_hasdbxref_hp.sssom.tsv",
"version": "http://purl.obolibrary.org/obo/mondo/releases/2026-09-01/mappings/mondo_hasdbxref_hp.sssom.tsv",
"version": "http://purl.obolibrary.org/obo/mondo/releases/2026-10-06/mappings/mondo_hasdbxref_hp.sssom.tsv",
"license": "https://creativecommons.org/publicdomain/zero/1.0/",
"type": "sssom",
"subject_source": {
Expand All @@ -728,7 +706,7 @@
"id": "https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv",
"name": "Biomappings",
"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.",
"version": "0.6.1-dev-5d3d419d",
"version": "0.6.1-dev-ed12b9f4",
"license": "https://creativecommons.org/publicdomain/zero/1.0/",
"type": "sssom",
"content_url": "https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv",
Expand Down Expand Up @@ -758,6 +736,22 @@
"status": "ok",
"metadata_completeness_score": 0.3182
},
{
"id": "https://github.com/biopragmatics/bioregistry/raw/refs/heads/main/exports/analyses/mapping_checking/mapping_embedding_similarities.tsv",
"name": "Bioregistry Mapping Similarity Analysis",
"license": "https://creativecommons.org/publicdomain/zero/1.0/",
"type": "sssom",
"content_url": "https://raw.githubusercontent.com/biopragmatics/bioregistry/refs/heads/main/exports/analyses/mapping_checking/mapping_embedding_similarities.sssom.tsv",
"registries": [
{
"id": "https://github.com/biopragmatics/mapping-registry",
"name": "Biopragmatics Mapping Registry",
"url": "https://github.com/biopragmatics"
}
],
"status": "ok",
"metadata_completeness_score": 0.3182
},
{
"id": "https://zenodo.org/records/15504009/files/mappings.sssom.tsv.gz",
"content_url": "https://zenodo.org/records/15504009/files/mappings.sssom.tsv.gz",
Expand Down Expand Up @@ -1298,6 +1292,25 @@
"status": "ok",
"metadata_completeness_score": 0.3815
},
{
"id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/amr-portal.sssom.tsv",
"description": "Manually curated antimicrobial name-to-ontology mappings from the AMR Portal",
"license": "https://w3id.org/sssom/license/unspecified",
"type": "sssom",
"subject_source": {
"id": "https://www.ebi.ac.uk/amr/"
},
"content_url": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/amr-portal.sssom.tsv",
"registries": [
{
"id": "https://w3id.org/sssom/commons/ebi-text-mappings",
"name": "EBI Text Mappings",
"url": "https://github.com/mapping-commons/ebi-text-mappings"
}
],
"status": "ok",
"metadata_completeness_score": 0.3815
},
{
"id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/faang.sssom.tsv",
"description": "FAANG project curated mappings",
Expand Down