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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 |
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Name |
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Description |
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VIVO/Scoring |
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Equivalence in RDF |
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Appears |
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In | ||||||
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E | MedlineCitation | Top Level element in a MedlineCitationSet and contains one publication | V | RDF Element
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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 |
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N/A |
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(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 |
| Main Citation (VD: not needed unless for scoring. We only want to pull in "completed") | ||
E | PMID | The Pubmed unique identifier | V |
| Main Citation | ||
E | DateCreated | The date the processing of the citation began. It has three sub elements Year, Month, and Day | S |
| Main Citation | ||
E | DateCompleted | Date processing of the record ends | S |
| Main Citation | ||
E | DateRevised | Identifies the date a change has been made. Only occurs in records that are MEDLINE, OLDMEDLINE, PubMed-not-MEDLINE | S |
| Main Citation | ||
E | Article | The wrapper around the non medline information about an article, like Authors and Title | N/A |
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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 |
| (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 |
| 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 |
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| 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 |
| Main Citation | ||
E | Issue | Identifies the issue that the journal resides in | V |
| 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 |
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E | Title | The title of the Journal that the article was published in | V |
| Journal Entry | ||
E | ISOAbbreviation | Used for linking from GenBank to PubMed |
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| (VD: N/A) | ||
E | ArticleTitle | The entire title of the Journal Article | V |
| Main Citation | ||
E | Pagination | The pages that the article occurred on | V |
| 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 |
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E | AbstractText | Actual Text of the abstract, not always available | V |
| Main Citation | ||
E | CopyrightInformation | Appears for articles where the publisher or author claim copyright on the citation | N/A |
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E | Affiliation | A string containing the afilliation information for the 1st Author | S |
| Main Citation | ||
E | AuthorList | Wrapper around the list of authors for a citation | N/A |
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E | Author | The Author of the Article in order as they appear in the publication sub elements include lastname, forename, suffix and initials | V |
| Individual Author | ||
E | LastName | The Surname of the author | V |
| Individual Author | ||
E | ForeName | The remainder of the name excluding the suffix, this is often only the initials of an individual spaced out | S |
| Individual Author | ||
E | Suffix | A persons suffix NOT honorific | S |
| Individual Author | ||
E | Initials | Often identical to the ForeName without spaces, this contains 2 initials for a person | S |
| 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 |
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? | 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 |
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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 |
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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 |
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E | MeshHeading | The individual Mesh Term for a publication, it has a descriptor and qualifier. | S |
| Mesh Term | ||
E | DescriptorName | The main term, if its a central concept of the paper its marked as MajorTopic. | S |
| Mesh Term | ||
E | QaulifierName | A sub heading of the Descriptor Name. | S |
| 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 |
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Database – map to core:Database
Dataset – map to vivo:Dataset
Diaries – map to bibo:Book
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Nurses' Instruction - DO NOT INCLUDE IN VIVO
Observational Study – map to bibo:Academic Article
Outlines - DO NOT INCLUDE IN VIVO
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Popular Works – DO NOT INCLUDE IN VIVO
Portraits – map to bibo:Image vivo:Article
Postcards - DO NOT INCLUDE IN VIVO
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Practice Guideline – map to bibo:Standard
Pragmatic Clinical Trial – map to bibo:Academic Article
Price Lists - DO NOT INCLUDE IN VIVO
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