{ "access": { "embargo": { "active": false, "reason": null }, "files": "public", "record": "public", "status": "open" }, "created": "2025-01-08T13:26:08.563757+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "files": { "count": 1, "enabled": true, "entries": { "pmdb_20250107_235055.tar": { "access": { "hidden": false }, "checksum": "md5:982cb97e14a981765665271da973a9f2", "ext": "tar", "id": "cef4ab71-c98b-4dc7-a964-7db2dd148fb3", "key": "pmdb_20250107_235055.tar", "links": { "content": "https://zenodo.org/api/records/14616021/files/pmdb_20250107_235055.tar/content", "self": "https://zenodo.org/api/records/14616021/files/pmdb_20250107_235055.tar" }, "metadata": {}, "mimetype": "application/x-tar", "size": 30659330560, "storage_class": "L" } }, "order": [], "total_bytes": 30659330560 }, "id": "14616021", "is_draft": false, "is_published": true, "links": { "access": "https://zenodo.org/api/records/14616021/access", "access_grants": "https://zenodo.org/api/records/14616021/access/grants", "access_links": "https://zenodo.org/api/records/14616021/access/links", "access_request": "https://zenodo.org/api/records/14616021/access/request", "access_users": "https://zenodo.org/api/records/14616021/access/users", "archive": "https://zenodo.org/api/records/14616021/files-archive", "archive_media": "https://zenodo.org/api/records/14616021/media-files-archive", "communities": "https://zenodo.org/api/records/14616021/communities", "communities-suggestions": "https://zenodo.org/api/records/14616021/communities-suggestions", "doi": "https://doi.org/10.5281/zenodo.14616021", "draft": "https://zenodo.org/api/records/14616021/draft", "file_modification": "https://zenodo.org/api/records/14616021/file-modification", "files": "https://zenodo.org/api/records/14616021/files", "latest": "https://zenodo.org/api/records/14616021/versions/latest", "latest_html": "https://zenodo.org/records/14616021/latest", "media_files": "https://zenodo.org/api/records/14616021/media-files", "parent": "https://zenodo.org/api/records/4008109", "parent_doi": "https://doi.org/10.5281/zenodo.4008109", "parent_doi_html": "https://zenodo.org/doi/10.5281/zenodo.4008109", "parent_html": "https://zenodo.org/records/4008109", "preview_html": "https://zenodo.org/records/14616021?preview=1", "quota_increase": "https://zenodo.org/api/records/14616021/quota-increase", "request_deletion": "https://zenodo.org/api/records/14616021/request-deletion", "requests": "https://zenodo.org/api/records/14616021/requests", "reserve_doi": "https://zenodo.org/api/records/14616021/draft/pids/doi", "self": "https://zenodo.org/api/records/14616021", "self_doi": "https://doi.org/10.5281/zenodo.14616021", "self_doi_html": "https://zenodo.org/doi/10.5281/zenodo.14616021", "self_html": "https://zenodo.org/records/14616021", "self_iiif_manifest": "https://zenodo.org/api/iiif/record:14616021/manifest", "self_iiif_sequence": "https://zenodo.org/api/iiif/record:14616021/sequence/default", "versions": "https://zenodo.org/api/records/14616021/versions" }, "media_files": { "count": 0, "enabled": false, "entries": {}, "order": [], "total_bytes": 0 }, "metadata": { "creators": [ { "affiliations": [ { "name": "Vanderbilt University Medical Center" } ], "person_or_org": { "family_name": "Hughey", "given_name": "Jacob", "identifiers": [ { "identifier": "0000-0002-1558-6089", "scheme": "orcid" } ], "name": "Hughey, Jacob", "type": "personal" } }, { "affiliations": [ { "name": "Vanderbilt University Medical Center" } ], "person_or_org": { "family_name": "Schoenbachler", "given_name": "Joshua", "identifiers": [ { "identifier": "0000-0001-8544-6359", "scheme": "orcid" } ], "name": "Schoenbachler, Joshua", "type": "personal" } } ], "description": "

The files constitute a compressed dump of PMDB, which was created in PostgreSQL 14 using the pmparser R package. Once you have a Postgres server running, you can set up the database as follows:

\n\n

1. Untar the file containing the database dump, which will create a folder. Substitute <tar_name> with the name of the tar file.

\n\n
tar xvf <tar_name> && rm <tar_name>
\n\n

2. Restore the database onto your Postgres server. Below is one way. Replace <...> as appropriate, substituting <dump_name> with the name of the new folder containing the dump files. This will take some time, so use as many cores as you can spare. Beware the full database is about 136 GB.

\n\n
createdb -h <host_name> -U <user_name> pmdb\npg_restore -j <num_cores> --no-privileges --no-owner -h <host_name> -U <user_name> -d pmdb <dump_name>
\n\n

MEDLINE/PubMed data are courtesy of the U.S. National Library of Medicine. See NLM's Terms and Conditions.

", "publication_date": "2025-01-08", "publisher": "Zenodo", "related_identifiers": [ { "identifier": "10.1101/2020.09.07.285924", "relation_type": { "id": "isreferencedby", "title": { "de": "Wird referenziert von", "en": "Is referenced by" } }, "resource_type": { "id": "publication-preprint", "title": { "de": "Preprint", "en": "Preprint" } }, "scheme": "doi" } ], "resource_type": { "id": "dataset", "title": { "de": "Datensatz", "en": "Dataset" } }, "rights": [ { "description": { "en": "" }, "id": "other-pd", "title": { "en": "Other (Public Domain)" } } ], "title": "PMDB: a relational database for PubMed" }, "parent": { "access": { "owned_by": { "user": "10752" }, "settings": { "accept_conditions_text": null, "allow_guest_requests": false, "allow_user_requests": false, "secret_link_expiration": 0 } }, "communities": { "default": "868c7e8c-c7dd-481a-b9a9-b8828299ffee", "entries": [ { "access": { "member_policy": "open", "members_visibility": "public", "record_submission_policy": "open", "review_policy": "open", "visibility": "public" }, "children": { "allow": false }, "created": "2019-05-01T19:45:24.860028+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "id": "868c7e8c-c7dd-481a-b9a9-b8828299ffee", "links": {}, "metadata": { "curation_policy": "

Curation is done manually by the community initiators.

\r\n", "page": "

This community is dealing with datasets, papers, code, and other resources in the scholarly field. Also resources concerning bibliometrics and scientometrics (e.g., publications' metadata, publications' full-texts, analyses of citation contexts, representations of publications) are welcome.

", "title": "Scholarly Data" }, "revision_id": 0, "slug": "scholarly-data", "updated": "2019-11-11T09:21:51.855384+00:00" } ], "ids": [ "868c7e8c-c7dd-481a-b9a9-b8828299ffee" ] }, "id": "4008109", "pids": { "doi": { "client": "datacite", "identifier": "10.5281/zenodo.4008109", "provider": "datacite" } } }, "pids": { "doi": { "client": "datacite", "identifier": "10.5281/zenodo.14616021", "provider": "datacite" }, "oai": { "identifier": "oai:zenodo.org:14616021", "provider": "oai" } }, "revision_id": 4, "stats": { "all_versions": { "data_volume": 55289250224572.0, "downloads": 3125, "unique_downloads": 2494, "unique_views": 11567, "views": 12185 }, "this_version": { "data_volume": 3924394311680.0, "downloads": 128, "unique_downloads": 115, "unique_views": 434, "views": 447 } }, "status": "published", "swh": {}, "updated": "2025-01-08T13:26:08.700727+00:00", "versions": { "index": 37, "is_latest": false } }