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Most tables are derived from the MEDLINE XML files, parsed according
to the MEDLINE®PubMed®
XML Element Descriptions and their Attributes. The
source column indicates the corresponding element in the
MEDLINE XML. All elements other than those for the pmid_status table and
the citation table are nested within the PubmedArticle element. “attr”
indicates a named attribute in the XML, and “int position” indicates an
integer to index each item in a list. The citation table is derived from
the NIH
Open Citation Collection.
| table_name | field_name | source |
|---|---|---|
| abstract | pmid | PMID |
| abstract | text | Abstract / AbstractText |
| abstract | label | Abstract / AbstractText / attr Label |
| abstract | nlm_category | Abstract / AbstractText / attr NlmCategory |
| abstract | abstract_pos | Abstract / AbstractText / int position |
| abstract_copyright | pmid | PMID |
| abstract_copyright | copyright | Abstract / CopyrightInformation |
| article | pmid | PMID |
| article | title | Article / ArticleTitle |
| article | language | Article / Language |
| article | vernacular_title | Article / VernacularTitle |
| article | pub_model | Article / attr PubModel |
| article | pub_date | Article / ArticleDate / Year-Month-Day |
| article_id | pmid | PMID |
| article_id | id_type | ArticleIdList / ArticleId / attr IdType |
| article_id | id_value | ArticleIdList / ArticleId |
| author | pmid | PMID |
| author | author_pos | AuthorList / Author / int position |
| author | last_name | AuthorList / Author / LastName |
| author | fore_name | AuthorList / Author / ForeName |
| author | initials | AuthorList / Author / Initials |
| author | suffix | AuthorList / Author / Suffix |
| author | valid | AuthorList / Author / attr ValidYN |
| author | equal_contrib | AuthorList / Author / attr EqualContrib |
| author | collective_name | AuthorList / Author / CollectiveName |
| author_affiliation | pmid | PMID |
| author_affiliation | author_pos | AuthorList / Author / int position |
| author_affiliation | affiliation_pos | AuthorList / Author / AffiliationInfo / Affiliation / int position |
| author_affiliation | affiliation | AuthorList / Author / AffiliationInfo / Affiliation |
| author_affiliation_identifier | pmid | PMID |
| author_affiliation_identifier | author_pos | AuthorList / Author / int position |
| author_affiliation_identifier | affiliation_pos | AuthorList / Author / Affiliation / int position |
| author_affiliation_identifier | source | AuthorList / Author / AffiliationInfo / Identifier / attr Source |
| author_affiliation_identifier | identifier | AuthorList / Author / AffiliationInfo / Identifier |
| author_identifier | pmid | PMID |
| author_identifier | author_pos | AuthorList / Author / int position |
| author_identifier | source | AuthorList / Author / Identifier / attr Source |
| author_identifier | identifier | AuthorList / Author / Identifier |
| author_list | pmid | PMID |
| author_list | complete | AuthorList / attr CompleteYN |
| chemical | pmid | PMID |
| chemical | registry_number | ChemicalList / Chemical / RegistryNumber |
| chemical | substance_name | ChemicalList / Chemical / NameOfSubstance |
| chemical | substance_ui | ChemicalList / Chemical / NameOfSubstance / attr UI |
| citation | citing_pmid | NIH OCC / citing |
| citation | cited_pmid | NIH OCC / referenced |
| citation_version | md5_computed | - |
| citation_version | pmparser_version | - |
| citation_version | datetime_processed | - |
| comment | pmid | PMID |
| comment | ref_type | CommentsCorrectionsList / CommentsCorrections / attr RefType |
| comment | ref_pmid | CommentsCorrectionsList / CommentsCorrections / PMID |
| data_bank | pmid | PMID |
| data_bank | data_bank_name | DataBankList / DataBank / DataBankName |
| data_bank | accession_number | DataBankList / DataBank / AccessionNumber |
| grant_item | pmid | PMID |
| grant_item | grant_id | GrantList / Grant / GrantID |
| grant_item | acronym | GrantList / Grant / Acronym |
| grant_item | agency | GrantList / Grant / Agency |
| grant_item | country | GrantList / Grant / Country |
| grant_list | pmid | PMID |
| grant_list | complete | GrantList / CompleteYN |
| investigator | pmid | PMID |
| investigator | investigator_pos | InvestigatorList / Investigator / int position |
| investigator | last_name | InvestigatorList / Investigator / LastName |
| investigator | fore_name | InvestigatorList / Investigator / ForeName |
| investigator | initials | InvestigatorList / Investigator / Initials |
| investigator | suffix | InvestigatorList / Investigator / Suffix |
| investigator | valid | InvestigatorList / Investigator / attr ValidYN |
| investigator_affiliation | pmid | PMID |
| investigator_affiliation | investigator_pos | InvestigatorList / Investigator / int position |
| investigator_affiliation | affiliation_pos | InvestigatorList / Investigator / AffiliationInfo / Affiliation / int position |
| investigator_affiliation | affiliation | InvestigatorList / Investigator / AffiliationInfo / Affiliation |
| investigator_affiliation_identifier | pmid | PMID |
| investigator_affiliation_identifier | investigator_pos | InvestigatorList / Investigator / int position |
| investigator_affiliation_identifier | affiliation_pos | InvestigatorList / Investigator / Affiliation / int position |
| investigator_affiliation_identifier | source | InvestigatorList / Investigator / AffiliationInfo / Identifier / attr Source |
| investigator_affiliation_identifier | identifier | InvestigatorList / Investigator / AffiliationInfo / Identifier |
| investigator_identifier | pmid | PMID |
| investigator_identifier | investigator_pos | InvestigatorList / Investigator / int position |
| investigator_identifier | source | InvestigatorList / Investigator / Identifier / attr Source |
| investigator_identifier | identifier | InvestigatorList / Investigator / Identifier |
| journal | pmid | PMID |
| journal | journal_name | Journal / Title |
| journal | journal_iso | Journal / ISOAbbreviation |
| journal | pub_date | Journal / Year-Month-Day |
| journal | pub_year | Journal / Year |
| journal | pub_month | Journal / Month |
| journal | pub_day | Journal / Day |
| journal | medline_date | Journal / MedlineDate |
| journal | volume | Journal / Volume |
| journal | issue | Journal / Issue |
| journal | cited_medium | Journal / JournalIssue / attr CitedMedium |
| keyword_item | pmid | PMID |
| keyword_item | keyword_name | KeywordList / Keyword |
| keyword_item | major_topic | KeywordList / Keyword / attr MajorTopicYN |
| keyword_list | pmid | PMID |
| keyword_list | list_owner | KeywordList / attr Owner |
| mesh_descriptor | pmid | PMID |
| mesh_descriptor | descriptor_pos | MeshHeadingList / MeshHeading / int position |
| mesh_descriptor | descriptor_name | MeshHeadingList / MeshHeading / DescriptorName |
| mesh_descriptor | descriptor_ui | MeshHeadingList / MeshHeading / DescriptorName / attr UI |
| mesh_descriptor | descriptor_major_topic | MeshHeadingList / MeshHeading / DescriptorName / attr MajorTopicYN |
| mesh_list | pmid | PMID |
| mesh_list | indexing_method | MedlineCitation / IndexingMethod |
| mesh_qualifier | pmid | PMID |
| mesh_qualifier | descriptor_pos | MeshHeadingList / MeshHeading / int position |
| mesh_qualifier | qualifier_name | MeshHeadingList / MeshHeading / QualifiierName |
| mesh_qualifier | qualifier_ui | MeshHeadingList / MeshHeading / QualifiierName / attr UI |
| mesh_qualifier | qualifier_major_topic | MeshHeadingList / MeshHeading / QualifiierName / attr MajorTopicYN |
| other_abstract | pmid | PMID |
| other_abstract | text | OtherAbstract / AbstractText |
| other_abstract | type | OtherAbstract / attr Type |
| other_abstract | language | OtherAbstract / attr Language |
| other_id | pmid | PMID |
| other_id | source | OtherId / attr Source |
| other_id | id_value | OtherId |
| pmid_status | pmid | PMID |
| pmid_status | version | PMID / attr Version |
| pmid_status | xml_filename | - |
| pmid_status | status | DeleteCitation | (MedlineCitation / attr Status) |
| pub_history | pmid | PMID |
| pub_history | pub_status | History / PubMedPubDate / attr PubStatus |
| pub_history | pub_date | History / PubMedPubDate / Year-Month-Day |
| pub_type | pmid | PMID |
| pub_type | type_name | PublicationTypeList / PublicationType |
| pub_type | type_id | PublicationTypeList / PublicationType / attr UI |
| readme | text | https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/README.txt |
| xml_processed | xml_filename | - |
| xml_processed | pmparser_version | - |
| xml_processed | datetime_processed | - |
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.