{ "access": { "embargo": { "active": false, "reason": null }, "files": "public", "record": "public", "status": "open" }, "created": "2026-04-09T15:32:59.532918+00:00", "custom_fields": { "code:codeRepository": "https://github.com/earth-metabolome-initiative/metrin-kg", "code:developmentStatus": { "id": "active", "title": { "en": "Active" } }, "code:programmingLanguage": [ { "id": "python", "title": { "en": "Python" } } ] }, "deletion_status": { "is_deleted": false, "status": "P" }, "files": { "count": 1, "enabled": true, "entries": { "metrin-kg.tar.gz": { "access": { "hidden": false }, "checksum": "md5:9c10d15a6c241bac30e9fe5305dac080", "ext": "gz", "id": "70e77803-84ee-4df9-b3bc-798127d789c2", "key": "metrin-kg.tar.gz", "links": { "content": "https://zenodo.org/api/records/19485732/files/metrin-kg.tar.gz/content", "self": "https://zenodo.org/api/records/19485732/files/metrin-kg.tar.gz" }, "metadata": {}, "mimetype": "application/gzip", "size": 3313161588, "storage_class": "L" } }, "order": [], "total_bytes": 3313161588 }, "id": "19485732", "is_draft": false, "is_published": true, "links": { "access": "https://zenodo.org/api/records/19485732/access", "access_grants": "https://zenodo.org/api/records/19485732/access/grants", "access_links": "https://zenodo.org/api/records/19485732/access/links", "access_request": "https://zenodo.org/api/records/19485732/access/request", "access_users": "https://zenodo.org/api/records/19485732/access/users", "archive": "https://zenodo.org/api/records/19485732/files-archive", "archive_media": "https://zenodo.org/api/records/19485732/media-files-archive", "communities": "https://zenodo.org/api/records/19485732/communities", "communities-suggestions": "https://zenodo.org/api/records/19485732/communities-suggestions", "doi": "https://doi.org/10.5281/zenodo.19485732", "draft": "https://zenodo.org/api/records/19485732/draft", "file_modification": "https://zenodo.org/api/records/19485732/file-modification", "files": "https://zenodo.org/api/records/19485732/files", "latest": "https://zenodo.org/api/records/19485732/versions/latest", "latest_html": "https://zenodo.org/records/19485732/latest", "media_files": "https://zenodo.org/api/records/19485732/media-files", "parent": "https://zenodo.org/api/records/15689186", "parent_doi": "https://doi.org/10.5281/zenodo.15689186", "parent_doi_html": "https://zenodo.org/doi/10.5281/zenodo.15689186", "parent_html": "https://zenodo.org/records/15689186", "preview_html": "https://zenodo.org/records/19485732?preview=1", "quota_increase": "https://zenodo.org/api/records/19485732/quota-increase", "request_deletion": "https://zenodo.org/api/records/19485732/request-deletion", "requests": "https://zenodo.org/api/records/19485732/requests", "reserve_doi": "https://zenodo.org/api/records/19485732/draft/pids/doi", "self": "https://zenodo.org/api/records/19485732", "self_doi": "https://doi.org/10.5281/zenodo.19485732", "self_doi_html": "https://zenodo.org/doi/10.5281/zenodo.19485732", "self_html": "https://zenodo.org/records/19485732", "self_iiif_manifest": "https://zenodo.org/api/iiif/record:19485732/manifest", "self_iiif_sequence": "https://zenodo.org/api/iiif/record:19485732/sequence/default", "versions": "https://zenodo.org/api/records/19485732/versions" }, "media_files": { "count": 0, "enabled": false, "entries": {}, "order": [], "total_bytes": 0 }, "metadata": { "creators": [ { "affiliations": [ { "id": "00vasag41", "identifiers": [ { "identifier": "00vasag41", "scheme": "ror" }, { "identifier": "grid.10711.36", "scheme": "grid" }, { "identifier": "0000 0001 2297 7718", "scheme": "isni" } ], "name": "University of Neuch\u00e2tel" } ], "person_or_org": { "family_name": "Tandon", "given_name": "Disha", "identifiers": [ { "identifier": "0009-0005-5515-1230", "scheme": "orcid" } ], "name": "Tandon, Disha", "type": "personal" } }, { "person_or_org": { "family_name": "Mendes de Farias", "given_name": "Tarcisio", "identifiers": [ { "identifier": "0000-0002-3175-5372", "scheme": "orcid" } ], "name": "Mendes de Farias, Tarcisio", "type": "personal" } }, { "affiliations": [ { "id": "022fs9h90", "identifiers": [ { "identifier": "022fs9h90", "scheme": "ror" }, { "identifier": "grid.8534.a", "scheme": "grid" }, { "identifier": "0000 0004 0478 1713", "scheme": "isni" } ], "name": "University of Fribourg" } ], "person_or_org": { "family_name": "Allard", "given_name": "Pierre-Marie", "identifiers": [ { "identifier": "0000-0003-3389-2191", "scheme": "orcid" } ], "name": "Allard, Pierre-Marie", "type": "personal" } }, { "affiliations": [ { "id": "00vasag41", "identifiers": [ { "identifier": "00vasag41", "scheme": "ror" }, { "identifier": "grid.10711.36", "scheme": "grid" }, { "identifier": "0000 0001 2297 7718", "scheme": "isni" } ], "name": "University of Neuch\u00e2tel" } ], "person_or_org": { "family_name": "defossez", "given_name": "emmanuel", "identifiers": [ { "identifier": "0000-0002-3279-9190", "scheme": "orcid" } ], "name": "defossez, emmanuel", "type": "personal" } } ], "description": "

Files associated with MEtabolomes, TRaits, and INteractions-Knowledge Graph (METRIN-KG). Contains input and output files used in mapping taxonomy, metadata, ontology and knowledge graph construction. Associated github repositories are metrin-kg and earth_metabolome_ontology

\n

Directory structure looks like the following. This directory can be used in combination with the code at the github repo metrin-kg, globi raw data and TRY database raw data.

\n

metrin-kg
\u2514\u2500\u2500 metrin-kg-data
    \u251c\u2500\u2500 case-studies
    \u2502   \u251c\u2500\u2500 CS1
    \u2502   \u2502   \u251c\u2500\u2500 CS1_viz.py
    \u2502   \u2502   \u251c\u2500\u2500 metrin-kg_APlx2T_q1.tsv
    \u2502   \u2502   \u251c\u2500\u2500 metrin-kg_CAIpHR_q2.tsv
    \u2502   \u2502   \u2514\u2500\u2500 metrin-kg_MptP26_q3.tsv
    \u2502   \u251c\u2500\u2500 CS2
    \u2502   \u2502   \u251c\u2500\u2500 CS2_viz.py
    \u2502   \u2502   \u2514\u2500\u2500 metrin-kg_ZVBghY_q4.tsv
    \u2502   \u251c\u2500\u2500 CS3
    \u2502   \u2502   \u251c\u2500\u2500 CS3_viz.py
    \u2502   \u2502   \u2514\u2500\u2500 metrin-kg_t49TVV_q5.tsv
    \u2502   \u251c\u2500\u2500 CS4
    \u2502   \u2502   \u251c\u2500\u2500 CS4_viz.py
    \u2502   \u2502   \u2514\u2500\u2500 metrin-kg_orF1qY_q6.tsv
    \u2502   \u2514\u2500\u2500 CS5
    \u2502       \u251c\u2500\u2500 CS5_viz.py
    \u2502       \u251c\u2500\u2500 metrin-kg_rtvxnd_q7.tsv
    \u2502       \u2514\u2500\u2500 metrin-kg_YEEGSZ_q8.tsv
    \u251c\u2500\u2500 ontology
    \u2502   \u2514\u2500\u2500 emi.ttl.gz
    \u251c\u2500\u2500 processed
    \u2502   \u251c\u2500\u2500 globi
    \u2502   \u2502   \u251c\u2500\u2500 correctedBiologicalSexNames.tsv
    \u2502   \u2502   \u251c\u2500\u2500 correctedBodyPartNamesGlobi.csv
    \u2502   \u2502   \u251c\u2500\u2500 correctedLifeStageNamesGlobi.csv
    \u2502   \u2502   \u251c\u2500\u2500 mappedBiologicalSexNames.tsv
    \u2502   \u2502   \u251c\u2500\u2500 unmappedBiologicalSexNames.tsv
    \u2502   \u2502   \u251c\u2500\u2500 verbatim_mappedBodyPartNamesGlobi.csv
    \u2502   \u2502   \u251c\u2500\u2500 verbatim_mappedLifeStageNamesGlobi.csv
    \u2502   \u2502   \u251c\u2500\u2500 verbatim_unmappedBodyPartNamesGlobi_mod.csv
    \u2502   \u2502   \u2514\u2500\u2500 verbatim_unmappedLifeStageNamesGlobi_mod.csv
    \u2502   \u251c\u2500\u2500 KG
    \u2502   \u2502   \u251c\u2500\u2500 enpkg-rdf-v4.tar.gz
    \u2502   \u2502   \u251c\u2500\u2500 examples_METRINKG-v0.1.ttl.gz
    \u2502   \u2502   \u251c\u2500\u2500 globi_output_w3id_v0.ttl.gz
    \u2502   \u2502   \u251c\u2500\u2500 taxonomy_output_v0.ttl.gz
    \u2502   \u2502   \u251c\u2500\u2500 trydb_output_w3id_v0.ttl.gz
    \u2502   \u2502   \u2514\u2500\u2500 void_METRINKG-v0.1.ttl.gz
    \u2502   \u251c\u2500\u2500 trydb
    \u2502   \u2502   \u251c\u2500\u2500 EmiMappingToTryDb.txt
    \u2502   \u2502   \u251c\u2500\u2500 qudtMappingToTryDb_full.txt
    \u2502   \u2502   \u2514\u2500\u2500 qudtMappingToTryDb.txt
    \u2502   \u251c\u2500\u2500 wdTax_duplicates.txt
    \u2502   \u251c\u2500\u2500 wdTax_GloBI.txt.gz
    \u2502   \u251c\u2500\u2500 wdTax_SPARQL_lineage_filtered_aligned.txt.gz
    \u2502   \u251c\u2500\u2500 wdTax_SPARQL_lineage_filtered.txt.gz
    \u2502   \u251c\u2500\u2500 wdTax_SPARQL_lineage.txt.gz
    \u2502   \u251c\u2500\u2500 wdTax_SPARQL.txt.gz
    \u2502   \u2514\u2500\u2500 wdTax_TRYdb.txt.gz
    \u2514\u2500\u2500 raw
        \u251c\u2500\u2500 enpkg_wd_pfId.csv.gz
        \u2514\u2500\u2500 Try20243712146549_TRY6.0_SpeciesList_TaxonomicHarmonization.csv

", "publication_date": "2026-04-09", "publisher": "Zenodo", "resource_type": { "id": "dataset", "title": { "de": "Datensatz", "en": "Dataset" } }, "rights": [ { "description": { "en": "CC0 waives copyright interest in a work you've created and dedicates it to the world-wide public domain. Use CC0 to opt out of copyright entirely and ensure your work has the widest reach." }, "icon": "cc-cc0-icon", "id": "cc0-1.0", "props": { "scheme": "spdx", "url": "https://creativecommons.org/publicdomain/zero/1.0/legalcode" }, "title": { "en": "Creative Commons Zero v1.0 Universal" } } ], "title": "METRIN-KG Data" }, "parent": { "access": { "owned_by": { "user": "1094354" }, "settings": { "accept_conditions_text": null, "allow_guest_requests": false, "allow_user_requests": false, "secret_link_expiration": 0 } }, "communities": { "default": "88bd9d39-827a-4217-adc8-cee55d57def9", "entries": [ { "access": { "member_policy": "open", "members_visibility": "public", "record_submission_policy": "open", "review_policy": "open", "visibility": "public" }, "children": { "allow": false }, "created": "2022-12-24T06:48:52.180241+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "id": "88bd9d39-827a-4217-adc8-cee55d57def9", "links": {}, "metadata": { "curation_policy": "

Curated by data@earthmetabolome.org

\r\n", "description": "A Zenodo Communities to gather data and outcomes of the Earth Metabolome Initiative.", "page": "", "title": "The Earth Metabolome Initiative" }, "revision_id": 0, "slug": "earth-metabolome", "updated": "2022-12-24T07:04:59.467037+00:00" } ], "ids": [ "88bd9d39-827a-4217-adc8-cee55d57def9" ] }, "id": "15689186", "pids": { "doi": { "client": "datacite", "identifier": "10.5281/zenodo.15689186", "provider": "datacite" } } }, "pids": { "doi": { "client": "datacite", "identifier": "10.5281/zenodo.19485732", "provider": "datacite" }, "oai": { "identifier": "oai:zenodo.org:19485732", "provider": "oai" } }, "revision_id": 4, "stats": { "all_versions": { "data_volume": 694407904501.0, "downloads": 193, "unique_downloads": 181, "unique_views": 555, "views": 604 }, "this_version": { "data_volume": 23192131116.0, "downloads": 7, "unique_downloads": 6, "unique_views": 24, "views": 25 } }, "status": "published", "swh": {}, "updated": "2026-04-09T15:32:59.852624+00:00", "versions": { "index": 7, "is_latest": true } }