com.aliasi.medline
Class MedlineCitation

java.lang.Object
  com.aliasi.medline.MedlineCitation

public class MedlineCitation
extends Object

A MedlineCitation represents the content of a single record in the 2008 MEDLINE database for the citation of an individual article.

A citation contains a richly structured set of information. Each citation contains an Article, which contains most of the information drawn from the article itself. The other information has been added by the creators of MEDLINE and comes in two flavors. The first type is information about the MEDLINE record itself, such as who "owns" it, when it was created, completed and revised, etc. The second type of information is metadata about the article itself, such as names of chemicals and database links, keywords, lists of MeSH terms, gene names and database links, cross-references to comments or corrections in other articles, etc.

In addition to the structured information in a citation the raw XML is available as a string through the xmlString() method.

Since:

LingPipe2.0

Version:

3.3

Author:

Bob Carpenter

Method Summary

Article	article() Returns the article for this citation, containing the information derived from the cited article itself.
Chemical[]	chemicals() Returns the array of chemical substances mentioned in this journal.
String[]	citationSubsets() Returns the array of citation subsets for this journal.
CommentOrCorrection[]	commentOrCorrections() Returns an array of the comments or corrections for this citation.
Date	dateCompleted() Returns the date that the processing of this citation ended or null if it is still in process.
Date	dateCreated() Returns the date on which this citation was created.
Date	dateRevised() Returns the latest date on which a change was made to this citation as a result of maintenance.
GeneralNote[]	generalNotes() Returns supplemental or descriptive information for this citation that does not fit elsewhere.
String[]	geneSymbols() Return an array of the gene symbols for this citation.
Investigator[]	investigators() Returns the investigators created by the (United States) National Aeronautics and Space Administration (NASA).
JournalInfo	journalInfo() Returns information about the journal in which this citation appears.
KeywordList[]	keywordLists() Returns the keyword lists for this citation.
MeshHeading[]	meshHeadings() Returns an array of MeSH headings for this citation.
String	nlmDcmsID() Returns the NLM DCMS identifier for this document.
String	numberOfReferences() Returns the number of bibliographic references in a review article, or the empty (zero length) string if none was provided.
OtherAbstract[]	otherAbstracts() Returns the array of other abstracts for this citation.
OtherID[]	otherIDs() Returns the array of other identifiers for this citation.
String	owner() The owner is the group that created and validated this citation.
static MedlineCitation	parse(InputSource inSource, XMLReader xmlReader)
PersonalNameSubject[]	personalNameSubjects() Returns the array of personal names of subjects for articles that contain information about the person named.
String	pmid() Returns the PubMed identifier for this document.
String[]	spaceFlightMissions() Returns a list of space flight names or mission numbers for articles on research carried out in space.
String	status() Returns the status of this citation.
String	toString() Returns a string-based representation of this citation.
String	xmlString() Returns the XML underlying this citation as a string.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Method Detail

xmlString

public String xmlString()

Returns the XML underlying this citation as a string. Note that there will be no XML declaration in this string, nor will there be a DTD reference. All entities and defaults provided by the DTD will be expanded into the string.

Returns:

The XML underlying this citation as a string.

owner

public String owner()

The owner is the group that created and validated this citation. Each citation has a unique owner, which takes on one of the following possible values, shown with their corresponding constants in MedlineCitationSet.

Value	Constant in MedlineCitationSet	Description	Notes
NLM	NLM_VALUE	(U.S.) National Library of Medicine, Index Section	Value for majority of citations
NASA	NASA_VALUE	(U.S.) National Aeronautics and Space Administration
PIP	PIP_VALUE	Population Information Program, Johns Hopkins	Not current; only on older citations
KIE	KIE_VALUE	Kennedy Institute of Ethics, Georgetown University
HSR	HSR_VALUE	(U.S.) National Infomration Center on Health Services Reserach and Health Care Technology, National Library of Medicine
HMD	HMD_VALUE	History of Medicine Division, National Library of Medicine
SIS	SIS_VALUE	Specialized Information Services Division, National Library of Medicine	Not yet used; reserved for future use.
NOTNLM	NOT_NLM_VALUE	Not from NLM	Will never be used for any distributed MEDLINE record

These values may also appear as owners of general notes and keyword lists.

Returns:

The owner of the group that created and validated this citation.

status

public String status()

Returns the status of this citation. The status is always defined, and takes one of the values listed below. As articles progress through the pipeline, they are rereleased with new status values; the later versions should replace the earlier ones based on PubMed identifier.

Value	Constant in MedlineCitationSet	Notes
In-Data-Review	IN_DATA_REVIEW_VALUE	Reference citation elements at the journal issue level have been checked against print or online versions. Citations with this status lack completion dates. They have not undergrone quality assurance nor had MeSH terms added.
In-Process	IN_PROCESS_VALUE	Citation elements at the article level have been reviewed, including author names, title and pagination. Not every in-process article is promoted to MEDLINE; some are classified out of scope and receive PubMed-not-Medline as their final status
Completed	COMPLETED_VALUE	These are 'true' MEDLINE records with date completed and typically with MeSH headings. This status remains under revisions.
PubMed-not-MEDLINE	PUBMED_NOT_MEDLINE_VALUE	These are articles have gone through data review, but were not chosen for inclusion. They fall into the following categories: (1) citations that precede the data a journal was selected for MEDLINE, (2) citations that are out of scope, and (3) analytical summaries of articles published elsewhere.
Publisher	PUBLISHER_VALUE	These are not distributed to licensees, and include a number of categories of yet-to-be processed, out of scope, and out of date articles.
MEDLINE	MEDLINE_VALUE	2005 addition not yet documented by the NLM.
OLDMEDLINE	MEDLINE_VALUE	2005 addition not yet documented by the NLM.

Returns:

The status of this citation.

nlmDcmsID

public String nlmDcmsID()

Returns the NLM DCMS identifier for this document. May return null if there is no identifier.

The PubMed identifier, available through the method pmid(), is the official identifier for MEDLINE documents.

Note that this identifier was introduced in 2005 and was previously known as the MEDLINE ID.

Returns:

The NLM DCMS identifier for this document.

pmid

public String pmid()

Returns the PubMed identifier for this document. This is now the official identifier for MEDLINE documents. Each document has a unique PubMed identifier, which will be a one to eight digit accession number without leading zeros. The identifiers of deleted records will not be reused.

Returns:

The PubMed identifier for this document.

dateCreated

public Date dateCreated()

Returns the date on which this citation was created. Note that this is not the date on which the article was created, but is the date on which the MEDLINE citation for the article was created. The value will be non-null because every citation is required to have a creation date. The date will only be resolved to the level of day, month and year.

Note that this is also not the same as the PubMed Entrez date, which is not distributed as part of MEDLINE.

Returns:

The date on which this citation was created.

dateCompleted

public Date dateCompleted()

Returns the date that the processing of this citation ended or null if it is still in process. Specifically, citations are completed when all extra information has been added and quality assurance has been completed. If a record's status is in-process, as indicated by method status(), it lacks a date completed, so that this method will return null. The date will only be resolved to the level of day, month and year.

For ciations before about the year 2000, the date created and date completed were set to the same value.

Returns:

The date that this citation was completed.

dateRevised

public Date dateRevised()

Returns the latest date on which a change was made to this citation as a result of maintenance. Note that no information is provided in MEDLINE as to the nature of the change, and only the latest revision date is included. The date will only be resolved to the level of day, month and year. The value may be null if this citation has not been revised.

Note that every record that existed at the time was revised on 18 December 2000, and many of these have been revised subsequently.

Returns:

The latest date on which a change was made to this citation.

article

public Article article()

Returns the article for this citation, containing the information derived from the cited article itself.

Returns:

The article for this citation.

journalInfo

public JournalInfo journalInfo()

Returns information about the journal in which this citation appears.

Returns:

Information about the journal in which this citation appears.

chemicals

public Chemical[] chemicals()

Returns the array of chemical substances mentioned in this journal. The array may be of length zero if no chemicals were included.

Returns:

The substances mentioned in this journal.

citationSubsets

public String[] citationSubsets()

Returns the array of citation subsets for this journal. These values indicate specialized subsets of the collection of journals.

AIM	citations from Abridged Index Medicus journals, a list of about 120 core clinical, English language journals.
B	citations from non-Index Medicus journals in the field of biotechnology (not currently used).
C	citations from non-Index Medicus journals in the field of communication disorders (not currently used).
D	citations from non-Index Medicus journals in the field of dentistry; these citations appeared in Index to Dental Literature.
E	citations in the field of bioethics. (includes records from the former BIOETHICS database)
F	older citations from one journal prior to its selection for Index Medicus; used to augment the database for NLM's International MEDLARS Centers (not currently used)
H	citations from non-Index Medicus journals in the field of health administration. (includes records from the former HealthSTAR database)
IM	citations from Index Medicus journals.
J	citations from non-Index Medicus journals in the field of population information. (not currently used; on records from the former POPLINE database)
K	citations from non-Index Medicus journals relating to consumer health.
N	citations from non-Index Medicus journals in the field of nursing; these citations appeared in the International Nursing Index.
R	citations from non-Index Medicus journals in the field of population and reproduction; these citations appeared in Population Sciences (not currently used).
Q	citations in the field of the history of medicine. (includes records from the former HISTLINE database)
QO	is subset of Q - indicates older history of medicine journal citations that were created before the former HISTLINE file was converted to a MEDLINE-like format. (For NLM use because they require special handling at NLM).
S	citations in the field of space life sciences. (includes records from the former SPACELINE database)
T	citations from non-Index Medicus journals in the field of health technology assessment. (includes records from the former HealthSTAR database)
X	citations in the field of AIDS/HIV. (includes records from the former AIDSLINE database)

Returns:

An array of zero or more citation subsets.

commentOrCorrections

public CommentOrCorrection[] commentOrCorrections()

Returns an array of the comments or corrections for this citation.

Returns:

The comments or corrections for this citaiton.

geneSymbols

public String[] geneSymbols()

Return an array of the gene symbols for this citation. This item was only provided for records processed at NLM between 1991 and 1995. Up to 25 symbols per article may appear. Each symbol is limited to 72 characters. There was no standardization of the naming conventions. SGML escapes appear in the text used for Greek characters. Superscripts are enclosed in <up> and </up> delimeters, whereas subscripts use down.

The Greek character entities used are listed in:

NLM Technical Bulletin: Greek Symbols

Returns:

An array of gene symbols for this citation.

meshHeadings

public MeshHeading[] meshHeadings()

Returns an array of MeSH headings for this citation.

Returns:

An array of MeSH headings for this citation.

numberOfReferences

public String numberOfReferences()

Returns the number of bibliographic references in a review article, or the empty (zero length) string if none was provided. Note that other information concerning reference counts are provided by NLM's partners as part of the general notes.

Returns:

Number of bibliographic references in a review article.

personalNameSubjects

public PersonalNameSubject[] personalNameSubjects()

Returns the array of personal names of subjects for articles that contain information about the person named. This is typically a biographical note or an obituary.

Returns:

An array of personal names of subjects in this article.

otherIDs

public OtherID[] otherIDs()

Returns the array of other identifiers for this citation. These identifiers are drawn from other sources as described in the documentation for OtherID.

Returns:

The array of other identifiers for this citation.

otherAbstracts

public OtherAbstract[] otherAbstracts()

Returns the array of other abstracts for this citation.

Returns:

The array of other abstracts for this citation.

keywordLists

public KeywordList[] keywordLists()

Returns the keyword lists for this citation. Each keyword list in the returned array will have an owner specified, and each keyword is specified as being a major or minor keyword.

Returns:

The keyword lists for this citation.

spaceFlightMissions

public String[] spaceFlightMissions()

Returns a list of space flight names or mission numbers for articles on research carried out in space. Results may be as simple as manned or short duration or may indicate more specific projects such as Biosatellite 2 Project.

This space flight data is added by the (United States) National Aeronautics and Space Administration (NASA) and more information is availabe from:

Space Flight Mission Summary Table

Returns:

An array of space flight names, descriptions or mission numbers.

investigators

public Investigator[] investigators()

Returns the investigators created by the (United States) National Aeronautics and Space Administration (NASA). Investigators identify NASA-funded principal investigators. Investigator lists are always complete.

Returns:

The inve

generalNotes

public GeneralNote[] generalNotes()

Returns supplemental or descriptive information for this citation that does not fit elsewhere. Each general note has an owner and text.

Returns:

The general notes for this citation.

toString

public String toString()

Returns a string-based representation of this citation.

Overrides:

toString in class Object

Returns:

A string-based representation of this citation.

parse

public static MedlineCitation parse(InputSource inSource,
                                    XMLReader xmlReader)
                             throws IOException,
                                    SAXException

Throws:

IOException

SAXException