Overview
The definition of attributes from Pubmed and their transformation to elements in the VIVO ontology's schema. PubMed uses the Medline schema for storing citations. Medline is the Medical Literature Analysis and Retrival System Online (Medlars Online).
Development Documents
Medline/PubMed Resource Guide - http://www.nlm.nih.gov/bsd/pmresources.html#data
Medline/PubMed XML Data Elments - http://www.nlm.nih.gov/bsd/licensee/data_elements_doc.html
XSLT Tutorial - http://www.w3schools.com/xsl/xsl_languages.asp
Xpath Tutorial - http://www.w3schools.com/xpath/default.asp
XSL-FO Tutorial - http://www.w3schools.com/xslfo/default.asp
Medline to VIVO
See also the attached xsl file (last updated 2013-12-09) for mapping Scopus and MEDLINE bibliographic records to VIVO. Note that there are some minor differences between the mappings below and the attached file.
Element/Attribute | Name | Description | VIVO/Scoring | Equivalence in RDF | Appears In |
---|---|---|---|---|---|
E | MedlineCitation | Top Level element in a MedlineCitationSet and contains one publication | V |
<rfd:Description>
|
RDF Element |
A | Owner | Attribute of Medline Citation, the owner of the article is the party responsible for creating and validating the citation. There are only 8 possible owners | NLM, NASA, PIP, KIE, HSR, HMD, SIS, NOTNLM | N/A | (VD: not necessary unless needed for scoring) |
A | Status | The status is the stage the citation is currently in there are seven values; Completed, In-Process, PubMed-not-Medline, In-Data-Review, Publisher, MEDLINE, OLDMEDLINE | S | <score:PubMedStatus> | Main Citation (VD: not needed unless for scoring. We only want to pull in "completed") |
E | PMID | The Pubmed unique identifier | V | <bibo:pmid> | Main Citation |
E | DateCreated | The date the processing of the citation began. It has three sub elements Year, Month, and Day | S | <score:DateCreated> | Main Citation |
E | DateCompleted | Date processing of the record ends | S | <score:DateCompleted> | Main Citation |
E | DateRevised | Identifies the date a change has been made. Only occurs in records that are MEDLINE, OLDMEDLINE, PubMed-not-MEDLINE | S | <score:DateRevised> | Main Citation |
E | Article | The wrapper around the non medline information about an article, like Authors and Title | N/A |
|
|
A | PubModel | This describes how the publication was distributed and is apart of Article. There exist four values; Print, Print-Electronic, Electronic, Electronic-Print | UnK |
| (VD: Change to N/A) |
E | Journal | The envelope around the Journal information about an Article | V | <rdf:Description rdf:about="http//vivoweb.org/PubMed/journal/j{ISSN}> | (VD: This is only an envelope. Not needed?) |
E | ISSN | The ISSN, International Standards Serial Number is an 8 charcater value that identifes the journal | V | <bibo:ISSN> | Journal Entry |
A | ISSNType | Journals that have multiple distributions have multiple ISSNs, there are two types; Print and Electronic | UnK |
| (VD: change to N/A) |
E | JournalIssue | Containes information about the specific issue the article resides in |
|
| Journal Entry (VD: N/A) |
A | CitationMedium | The medium that was used to process the article. Two values; Internet or Print | UnK |
| (VD: N/A) |
E | Volume | The volume number that the article resides | V | <bibo:volume> | Main Citation |
E | Issue | Identifies the issue that the journal resides in | V | <bibo:issue> | Main Citation |
E | PubDate | The publication date for the article has sub elements, year, month, and day and medlinedate | UnK |
| (VD: data should be parsed into core:year, core:yearMonth, and core:date) |
E | MedlineDate | Dates that can not be parsed will be found in this sub element of PubDate | N/A |
|
|
E | Title | The title of the Journal that the article was published in | V | <core:Title> | Journal Entry |
E | ISOAbbreviation | Used for linking from GenBank to PubMed |
|
| (VD: N/A) |
E | ArticleTitle | The entire title of the Journal Article | V | <core:Title> | Main Citation |
E | Pagination | The pages that the article occurred on | V | <bibo:pages><bibo:pageStart><bibo:pageEnd> | Main Citation |
E | ElocationID | Procides an electronic location for items which lack standard page numbers | UnK |
| (VD: N/A) |
E | Abstract | Wrapper around information about the Abstract | N/A |
|
|
E | AbstractText | Actual Text of the abstract, not always available | V | <bibo:abstract> | Main Citation |
E | CopyrightInformation | Appears for articles where the publisher or author claim copyright on the citation | N/A |
|
|
E | Affiliation | A string containing the afilliation information for the 1st Author | S | <score:Affiliation > | Main Citation |
E | AuthorList | Wrapper around the list of authors for a citation | N/A |
|
|
E | Author | The Author of the Article in order as they appear in the publication sub elements include lastname, forename, suffix and initials | V | <rdf:Description><rdf:Type foaf:Person /> | Individual Author |
E | LastName | The Surname of the author | V | <foaf:lastName> | Individual Author |
E | ForeName | The remainder of the name excluding the suffix, this is often only the initials of an individual spaced out | S | <score:foreName> | Individual Author |
E | Suffix | A persons suffix NOT honorific | S | <score:suffix> | Individual Author |
E | Initials | Often identical to the ForeName without spaces, this contains 2 initials for a person | S | <score:initials | Individual Author |
E | Language | Three letter description of the language the article was published in | UnK |
| (VD: N/A) |
E | Databank | Contains information pertaining to the registration of several types of data. this data includes: molecular sequence data, clinical trial numbers, gene expression/molecular abundance data, and PubChem. This field is being ignored for now. | N/A |
|
|
? | DOI | This is the DOI, as listed in PubMed. | ? |
| (VD: use bibo:doi) |
E | GrantList | Wrapper for the list of grants related to the publication. | N/A |
|
|
E | Grant | Wrapper for the information about a single grant. Expect Inclusion of this data property in milestone 4. | UnK |
| Individual Grant (VD: N/A) |
E | GrantID | The contract number of the grant | UnK |
| Individual Grant (VD: Is it possible to link a publication entity to a grant entity using the grant ID property "core:sponsorAwardId") |
E | Acronym | The 2 letter acronym of the grant | UnK |
| Individual Grant (VD: N/A) |
E | Agency | The agency that supplied the grant | UnK |
| Individual Grant (VD: N/A) |
E | Country | Country of the grant agency | UnK |
| Individual Grant (VD: N/A) |
E | PublicationTypeList | Wrapper containing a list of article types | N/A |
|
|
E | PublicationType | V | see below for map of types to vivo classes | Main Citation | |
E | VernacularTitle | The title of the publication in its originating language. | UnK |
| (VD: N/A) |
E | ArticleDate | the date the publisher made an electronic version of the article | UnK |
| (VD: N/A) |
E | Country | the country the article was published in | UnK |
| (VD: N/A) |
E | MedlineTA | The Medline Title Abbreviation for the Journal. The site http://www.nlm.nih.gov/pubs/factsheets/constructitle.htmlcontains all of the rules used by NLM to abbreviate a title. | UnK |
| (VD: N/A) |
E | NlmUniqueID | the accession number for the journal the article was written in. | UnK |
| (VD: N/A) |
E | ISSNLinking | the ISSN designated by the ISSN Network to enable co-location or linking among the different media versions of a continueing resource | UnK |
| (VD: N/A) |
E | ChemicalList | The wrapper for a list of chemicals | UnK |
| (VD: N/A) |
E | Chemical | the chemical being specified in the NLM record | UnK |
| (VD: use core:freetextKeyword) |
E | Registry Number | a unique 5-9 digit number in a hyphenated format assigned by the Chemical Abstract Services. | UnK |
| (VD: N/A) |
E | Name of Substance | the name of the substance that the registry number identifies | UnK |
| (VD: use core:freetextKeyword) |
E | CitationSubset | The subset that Medline records from certain sources or on certain topics were assigned. | UnK |
| (VD: N/A) |
E | CommentsCorrections | This section details various citation notes, its unknown how this would be used by scoring and even more unknown if its needed in the main citation on VIVO. | UnK |
| (VD: N/A) |
E | GeneSymbolList | The wrapper for gene's listed in a publication | UnK |
| (VD: N/A) |
E | GeneSymbol | The abbreviated form of the gene name as reported in the literature | UnK |
| (VD: N/A) |
E | MeshHeadingList | Wrapper for the list of Mesh Terms associated with an article | N/A |
|
|
E | MeshHeading | The individual Mesh Term for a publication, it has a descriptor and qualifier. | S | <rdf:Description><rdf:Type score:MeshTerm> | Mesh Term |
E | DescriptorName | The main term, if its a central concept of the paper its marked as MajorTopic. | S | <score:Descriptor> | Mesh Term |
E | QaulifierName | A sub heading of the Descriptor Name. | S | <score:Qualifier | Mesh Term |
E | NumberOfReferences | Number of Bibliographic references in the article | N/A |
| (VD: N/A) |
E | PersonalNameSubjectList | The names of people that appear in the article (such as biographical notes or obituaryies). | N/A |
| (VD: N/A) |
E | OtherID | ID's of other collaborating partners with NLM. This information is not used at the present time but may be added later. | UnK |
| (VD: N/A) |
E | OtherAbstract | Alternative abstracts created by a collaborating partner or other entity | UnK |
| (VD: N/A) |
E | KeywordList | A list of Keywords assigned by a collaborating data producer, or in the case of oldmedline before there was mesh by NLM itself. | UnK |
| (VD: use core:freetextKeyword) |
E | SpaceFlightMission | If a citation was created by NASA it may come with information on the space flight mission that the research was conducted on. | UnK |
| (VD: N/A) |
E | InvestigatorList | For citations created by NASA originally, and other data partners later, the investigator is the PI on the grant that the research was produced. This is stored in the same format as the Author list | UnK |
| (VD: N/A) |
E | GeneralNote | Descriptive information provided by an NLM partner. | UnK |
| (VD: N/A) |
E | DeleteCitation | Most of the data is removed, but the stub is marked as deleted. We shouldn't be ingesting these publications. | N/A |
|
Publication Type Translation
Publication Characteristics (Publication Types) - Scope Notes
Abbreviations – DO NOT INCLUDE IN VIVO
Abstracts - DO NOT INCLUDE IN VIVO
Academic Dissertations - DO NOT INCLUDE IN VIVO
Account Books - DO NOT INCLUDE IN VIVO
Addresses – map to core:Conference Paper
Advertisements - DO NOT INCLUDE IN VIVO
Almanacs - DO NOT INCLUDE IN VIVO
Anecdotes - DO NOT INCLUDE IN VIVO
Animation - DO NOT INCLUDE IN VIVO
Annual Reports - DO NOT INCLUDE IN VIVO
Aphorisms and Proverbs - DO NOT INCLUDE IN VIVO
Architectural Drawings - DO NOT INCLUDE IN VIVO
Atlases – map to bibo:Reference Source
Bibliography – map to bibo:Academic Article
Biobibliography - map to bibo:Academic Article
Biography – map to bibo:Book
Book Illustrations - DO NOT INCLUDE IN VIVO
Book Reviews – map to core:Review
Bookplates - DO NOT INCLUDE IN VIVO
Broadsides - DO NOT INCLUDE IN VIVO
Caricatures - DO NOT INCLUDE IN VIVO
Cartoons - DO NOT INCLUDE IN VIVO
Case Reports – map to core:Case Study
Catalogs - DO NOT INCLUDE IN VIVO
Charts – map to bibo:Image
Chronology - DO NOT INCLUDE IN VIVO
Classical Article – map to bibo:Academic Article
Clinical Conference – map to bibo:Academic Article
Clinical Trial – map to bibo:Academic Article
Clinical Trial, Phase I - map to bibo:Academic Article
Clinical Trial, Phase II - map to bibo:Academic Article
Clinical Trial, Phase III - map to bibo:Academic Article
Clinical Trial, Phase IV - map to bibo:Academic Article
Collected Correspondence – map to bibo:Article and bibo:Book
Collected Works - map to bibo:Article and bibo:Book
Collections - DO NOT INCLUDE IN VIVO
Comment – map to bibo:Academic Article
Comparative Study – map to bibo:Academic Article
Congresses – map to bibo:Proceedings
Consensus Development Conference – map to bibo:Proceedings
Consensus Development Conference, NIH – map to bibo:Proceedings
Controlled Clinical Trial – map to bibo:Academic Article
Cookbooks – map to bibo:Book
Corrected and Republished Article - map to bibo:Academic Article
Database – map to core:Database
Dataset – map to vivo:Dataset
Diaries – map to bibo:Book
Dictionary – map to bibo:Reference Source
Directory - map to bibo:Reference Source
Documentaries and Factual Films – map to bibo:Film
Drawings – map to bibo:Image
Duplicate Publication – map to bibo:Article and bibo:Book
Editorial – map to core:Editorial Article
Encyclopedias - map to bibo:Reference Source
English Abstract - DO NOT INCLUDE IN VIVO
Ephemera - DO NOT INCLUDE IN VIVO
Essays – map to bibo:Article and bibo:Book
Eulogies - DO NOT INCLUDE IN VIVO
Evaluation Studies – map to bibo:Academic Article
Examination Questions - DO NOT INCLUDE IN VIVO
Exhibitions - DO NOT INCLUDE IN VIVO
Festschrift – map to bibo:Book
Fictional Works – map to bibo:Article and bibo:Book
Forms - DO NOT INCLUDE IN VIVO
Formularies – map to bibo:Book
Funeral Sermons - DO NOT INCLUDE IN VIVO
Government Publications – new publication class needed
Guidebooks – map to bibo:Reference Source
Guideline – map to bibo:Standard
Handbooks – map to bibo:Reference Source
Herbals - DO NOT INCLUDE IN VIVO
Historical Article – map to bibo:Article
Humor - DO NOT INCLUDE IN VIVO
In Vitro - DO NOT INCLUDE IN VIVO
Incunabula – map to bibo:Book
Indexes – map to bibo:Reference Source
Instruction – map to bibo:Audio Visual Document
Interactive Tutorial – need new pub class for multimedia
Interview – map to bibo:Book and bibo:Article
Introductory Journal Article – map to bibo:Article
Journal Article – map to bibo:Academic Article
Juvenile Literature - DO NOT INCLUDE IN VIVO
Laboratory Manuals - DO NOT INCLUDE IN VIVO
Lecture Notes - DO NOT INCLUDE IN VIVO
Lectures – need new pub class for speeches??
Legal Cases – map to bibo:Legal Case Document
Legislation – map to bibo:Legislation
Letter - DO NOT INCLUDE IN VIVO
Manuscripts - DO NOT INCLUDE IN VIVO
Maps – map to bibo:Map
Meeting Abstracts – map to bibo:Conference Proceedings
Meta-Analysis – map to bibo:Academic Article
Monograph - DO NOT INCLUDE IN VIVO
Multicenter Study – map to bibo:Academic Article
News – map to bibo:Article
Newspaper Article – map to bibo:Article
Nurses' Instruction - DO NOT INCLUDE IN VIVO
Observational Study – map to bibo:Academic Article
Outlines - DO NOT INCLUDE IN VIVO
Overall - DO NOT INCLUDE IN VIVO
Patents – map to bibo:Patent
Patient Education Handout – map to bibo:Document
Periodical Index – map to bibo:Reference Source
Periodicals – map to bibo:Periodical
Personal Narratives - DO NOT INCLUDE IN VIVO
Pharmacopoeias – map to bibo:Reference Source
Phrases - DO NOT INCLUDE IN VIVO
Pictorial Works – map to bibo:Article and bibo:Book
Poetry - DO NOT INCLUDE IN VIVO
Popular Works – DO NOT INCLUDE IN VIVO
Portraits – map to bibo:Image vivo:Article
Postcards - DO NOT INCLUDE IN VIVO
Posters - DO NOT INCLUDE IN VIVO
Practice Guideline – map to bibo:Standard
Pragmatic Clinical Trial – map to bibo:Academic Article
Price Lists - DO NOT INCLUDE IN VIVO
Problems and Exercises - DO NOT INCLUDE IN VIVO
Programmed Instruction - DO NOT INCLUDE IN VIVO
Programs - DO NOT INCLUDE IN VIVO
Prospectuses - DO NOT INCLUDE IN VIVO
Publication Components - DO NOT INCLUDE IN VIVO
Publication Formats - DO NOT INCLUDE IN VIVO
Published Erratum - DO NOT INCLUDE IN VIVO
Randomized Controlled Trial – map to bibo:Academic Article
Research Support, American Recovery and Reinvestment Act - DO NOT INCLUDE IN VIVO
Research Support, N.I.H., Extramural - DO NOT INCLUDE IN VIVO
Research Support, N.I.H., Intramural - DO NOT INCLUDE IN VIVO
Research Support, Non-U.S. Gov't - DO NOT INCLUDE IN VIVO
Research Support, U.S. Gov't, Non-P.H.S. - DO NOT INCLUDE IN VIVO
Research Support, U.S. Gov't, P.H.S. - DO NOT INCLUDE IN VIVO
Resource Guides - DO NOT INCLUDE IN VIVO
Retracted Publication - DO NOT INCLUDE IN VIVO
Retraction of Publication - DO NOT INCLUDE IN VIVO
Review – map to core:Review and bibo:Book
Scientific Integrity Review - DO NOT INCLUDE IN VIVO
Sermons - DO NOT INCLUDE IN VIVO
Statistics – map to bibo:Book and bibo:Article
Study Characteristics – map to bibo:Article
Support of Research - DO NOT INCLUDE IN VIVO
Tables - DO NOT INCLUDE IN VIVO
Technical Report – map to bibo:Report
Terminology - DO NOT INCLUDE IN VIVO
Textbooks – map to bibo:Book
Twin Study – map to bibo:Academic Article
Unedited Footage - DO NOT INCLUDE IN VIVO
Union Lists - DO NOT INCLUDE IN VIVO
Unpublished Works - DO NOT INCLUDE IN VIVO
Validation Studies - map to bibo:Academic Article
Webcasts - need new pub class for multimedia