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Update mappings from biomappings org
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‎data/mapping-specifications.json‎

Lines changed: 286 additions & 4 deletions
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@@ -233,7 +233,7 @@
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},
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{
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"id": "http://purl.obolibrary.org/obo/mondo/mappings/mondo_hasdbxref_icd10cm.sssom.tsv",
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"version": "http://purl.obolibrary.org/obo/mondo/releases/2026-03-03/mappings/mondo_hasdbxref_icd10cm.sssom.tsv",
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"version": "http://purl.obolibrary.org/obo/mondo/releases/2026-04-07/mappings/mondo_hasdbxref_icd10cm.sssom.tsv",
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"license": "https://creativecommons.org/publicdomain/zero/1.0/",
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"type": "sssom",
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"subject_source": {
@@ -269,7 +269,7 @@
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"id": "https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv",
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"name": "Biomappings",
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"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.",
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"version": "0.5.0-dev-528eae3f",
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"version": "0.5.1-dev-ec7849df",
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"license": "https://creativecommons.org/publicdomain/zero/1.0/",
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"type": "sssom",
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"content_url": "http://w3id.org/sssom/commons/monarch/mappings/mesh_chebi_biomappings.sssom.tsv",
@@ -400,7 +400,7 @@
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},
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{
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"id": "http://purl.obolibrary.org/obo/mondo/mappings/mondo_hasdbxref_hp.sssom.tsv",
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"version": "http://purl.obolibrary.org/obo/mondo/releases/2026-03-03/mappings/mondo_hasdbxref_hp.sssom.tsv",
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"version": "http://purl.obolibrary.org/obo/mondo/releases/2026-04-07/mappings/mondo_hasdbxref_hp.sssom.tsv",
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"license": "https://creativecommons.org/publicdomain/zero/1.0/",
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"type": "sssom",
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"subject_source": {
@@ -543,7 +543,7 @@
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},
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{
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"id": "http://purl.obolibrary.org/obo/mondo/mappings/mondo_hasdbxref_hp.sssom.tsv",
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"version": "http://purl.obolibrary.org/obo/mondo/releases/2026-03-03/mappings/mondo_hasdbxref_hp.sssom.tsv",
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"version": "http://purl.obolibrary.org/obo/mondo/releases/2026-04-07/mappings/mondo_hasdbxref_hp.sssom.tsv",
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"license": "https://creativecommons.org/publicdomain/zero/1.0/",
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"type": "sssom",
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"subject_source": {
@@ -559,6 +559,288 @@
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],
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"fair_score": 0.4042
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},
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{
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"id": "https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv",
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"name": "Biomappings",
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"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.",
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"version": "0.5.1-dev-ec7849df",
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"license": "https://creativecommons.org/publicdomain/zero/1.0/",
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"type": "sssom",
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"content_url": "https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv",
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"registries": [
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{
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"id": "https://github.com/biopragmatics/mapping-registry",
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"name": "Biopragmatics Mapping Registry"
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}
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],
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"fair_score": 0.4773
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},
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{
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"id": "https://github.com/biopragmatics/bioregistry/raw/main/exports/sssom/bioregistry.sssom.tsv",
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"name": "Bioregistry",
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"license": "https://creativecommons.org/publicdomain/zero/1.0/",
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"type": "sssom",
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"content_url": "https://github.com/biopragmatics/bioregistry/raw/refs/heads/main/exports/sssom/bioregistry.sssom.tsv",
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"registries": [
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{
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"id": "https://github.com/biopragmatics/mapping-registry",
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"name": "Biopragmatics Mapping Registry"
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}
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],
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"fair_score": 0.3182
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},
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{
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"id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/sysmicro.sssom.tsv",
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"description": "Curated cellular microscopy phenotype mappings from SysMicro",
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"license": "https://w3id.org/sssom/license/unspecified",
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"type": "sssom",
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"subject_source": {
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"id": "https://www.ebi.ac.uk/fg/sym"
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},
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"content_url": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/sysmicro.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/ebi-text-mappings",
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"name": "EBI Text Mappings",
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"url": "https://github.com/mapping-commons/ebi-text-mappings"
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}
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],
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"fair_score": 0.3815
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},
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{
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"id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/atlas.sssom.tsv",
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"description": "Curated text-to-ontology mappings from Expression Atlas",
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"license": "https://w3id.org/sssom/license/unspecified",
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"type": "sssom",
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"subject_source": {
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"id": "https://www.ebi.ac.uk/gxa"
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},
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"content_url": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/atlas.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/ebi-text-mappings",
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"name": "EBI Text Mappings",
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"url": "https://github.com/mapping-commons/ebi-text-mappings"
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}
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],
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"fair_score": 0.3815
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},
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{
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"id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/ebisc.sssom.tsv",
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"description": "Curated text-to-ontology mappings from EBiSC",
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"license": "https://w3id.org/sssom/license/unspecified",
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"type": "sssom",
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"subject_source": {
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"id": "https://cells.ebisc.org/"
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},
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"content_url": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/ebisc.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/ebi-text-mappings",
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"name": "EBI Text Mappings",
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"url": "https://github.com/mapping-commons/ebi-text-mappings"
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}
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],
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"fair_score": 0.3815
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},
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{
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"id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/cttv.sssom.tsv",
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"description": "Curated disease indication mappings from Open Targets",
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"license": "https://w3id.org/sssom/license/unspecified",
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"type": "sssom",
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"subject_source": {
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"id": "https://www.targetvalidation.org"
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},
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"content_url": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/cttv.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/ebi-text-mappings",
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"name": "EBI Text Mappings",
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"url": "https://github.com/mapping-commons/ebi-text-mappings"
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}
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],
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"fair_score": 0.3815
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},
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{
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"id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/uniprot.sssom.tsv",
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"description": "Curated disease mappings from UniProt",
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"license": "https://w3id.org/sssom/license/unspecified",
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"type": "sssom",
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"subject_source": {
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"id": "https://www.ebi.ac.uk/uniprot"
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},
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"content_url": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/uniprot.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/ebi-text-mappings",
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"name": "EBI Text Mappings",
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"url": "https://github.com/mapping-commons/ebi-text-mappings"
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}
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],
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"fair_score": 0.3815
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},
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{
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"id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/eva-clinvar.sssom.tsv",
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"description": "EVA ClinVar disease mappings",
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"license": "https://w3id.org/sssom/license/unspecified",
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"type": "sssom",
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"subject_source": {
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"id": "https://www.ebi.ac.uk/eva"
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},
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"content_url": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/eva-clinvar.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/ebi-text-mappings",
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"name": "EBI Text Mappings",
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"url": "https://github.com/mapping-commons/ebi-text-mappings"
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}
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],
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"fair_score": 0.3815
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},
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{
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"id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/cbi.sssom.tsv",
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"description": "Curated plant biosample mappings",
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"license": "https://w3id.org/sssom/license/unspecified",
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"type": "sssom",
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"subject_source": {
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"id": "https://www.ebi.ac.uk/biosamples"
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},
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"content_url": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/cbi.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/ebi-text-mappings",
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"name": "EBI Text Mappings",
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"url": "https://github.com/mapping-commons/ebi-text-mappings"
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}
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],
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"fair_score": 0.3815
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},
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{
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"id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/clinvar-xrefs.sssom.tsv",
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"description": "ClinVar cross-reference mappings",
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"license": "https://w3id.org/sssom/license/unspecified",
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"type": "sssom",
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"subject_source": {
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"id": "https://www.ncbi.nlm.nih.gov/clinvar"
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},
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"content_url": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/clinvar-xrefs.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/ebi-text-mappings",
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"name": "EBI Text Mappings",
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"url": "https://github.com/mapping-commons/ebi-text-mappings"
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}
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],
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"fair_score": 0.3815
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},
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{
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"id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/metabolights.sssom.tsv",
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"description": "Curated metabolomics mappings from MetaboLights",
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"license": "https://w3id.org/sssom/license/unspecified",
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"type": "sssom",
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"subject_source": {
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"id": "https://www.ebi.ac.uk/metabolights"
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},
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"content_url": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/metabolights.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/ebi-text-mappings",
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"name": "EBI Text Mappings",
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"url": "https://github.com/mapping-commons/ebi-text-mappings"
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}
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],
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"fair_score": 0.3815
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},
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{
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"id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/ukbiobank.sssom.tsv",
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"description": "UK Biobank phenotype mappings to EFO",
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"license": "https://w3id.org/sssom/license/unspecified",
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"type": "sssom",
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"subject_source": {
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"id": "https://github.com/EBISPOT/EFO-UKB-mappings"
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},
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"content_url": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/ukbiobank.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/ebi-text-mappings",
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"name": "EBI Text Mappings",
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"url": "https://github.com/mapping-commons/ebi-text-mappings"
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}
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],
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"fair_score": 0.3815
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},
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{
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"id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/ebi-biosamples.sssom.tsv",
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"description": "Curated BioSamples text-to-ontology mappings",
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"license": "https://w3id.org/sssom/license/unspecified",
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"type": "sssom",
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"subject_source": {
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"id": "https://www.ebi.ac.uk/biosamples/"
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},
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"content_url": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/ebi-biosamples.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/ebi-text-mappings",
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"name": "EBI Text Mappings",
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"url": "https://github.com/mapping-commons/ebi-text-mappings"
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}
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],
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"fair_score": 0.3815
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},
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{
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"id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/faang.sssom.tsv",
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"description": "FAANG project curated mappings",
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"license": "https://w3id.org/sssom/license/unspecified",
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"type": "sssom",
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"subject_source": {
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"id": "https://www.ebi.ac.uk/vg/faang"
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},
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"content_url": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/faang.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/ebi-text-mappings",
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"name": "EBI Text Mappings",
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"url": "https://github.com/mapping-commons/ebi-text-mappings"
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}
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],
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"fair_score": 0.3815
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},
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{
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"id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/hca.sssom.tsv",
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"description": "Human Cell Atlas curated mappings",
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"license": "https://w3id.org/sssom/license/unspecified",
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"type": "sssom",
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"subject_source": {
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"id": "https://www.ebi.ac.uk/about/collaborations/human-cell-atlas"
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},
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"content_url": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/hca.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/ebi-text-mappings",
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"name": "EBI Text Mappings",
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"url": "https://github.com/mapping-commons/ebi-text-mappings"
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}
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],
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"fair_score": 0.3815
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},
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{
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"id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/gwas.sssom.tsv",
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"description": "GWAS Catalog trait-to-EFO mappings",
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"license": "https://w3id.org/sssom/license/unspecified",
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"type": "sssom",
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"subject_source": {
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"id": "http://www.ebi.ac.uk/gwas"
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},
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"content_url": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/gwas.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/ebi-text-mappings",
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"name": "EBI Text Mappings",
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"url": "https://github.com/mapping-commons/ebi-text-mappings"
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}
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],
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"fair_score": 0.3815
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},
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{
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"id": "https://w3id.org/mapping-commons/fair/mappingspecification/sssom-to-fair-mappings",
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"name": "SSSOM to FAIR Mappings Schema Transformation",

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