com.aliasi.medline
Class MedlineCitation

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

Deprecated. Moved to lingmed sandbox project.

@Deprecated
public class MedlineCitation
extends Object

A MedlineCitation represents the content of a single record in the 2009 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:
3.9.1
Author:
Bob Carpenter

Method Summary
 Article article()
          Deprecated. See class documentation.
 Chemical[] chemicals()
          Deprecated. See class documentation.
 String[] citationSubsets()
          Deprecated. Returns the array of citation subsets for this journal.
 CommentOrCorrection[] commentOrCorrections()
          Deprecated. See class documentation.
 Date dateCompleted()
          Deprecated. Returns the date that the processing of this citation ended or null if it is still in process.
 Date dateCreated()
          Deprecated. Returns the date on which this citation was created.
 Date dateRevised()
          Deprecated. Returns the latest date on which a change was made to this citation as a result of maintenance.
 GeneralNote[] generalNotes()
          Deprecated. See class documentation.
 String[] geneSymbols()
          Deprecated. Return an array of the gene symbols for this citation.
 Investigator[] investigators()
          Deprecated. See class documentation.
 JournalInfo journalInfo()
          Deprecated. See class documentation.
 KeywordList[] keywordLists()
          Deprecated. See class documentation.
 MeshHeading[] meshHeadings()
          Deprecated. See class documentation.
 String nlmDcmsID()
          Deprecated. Returns the NLM DCMS identifier for this document.
 String numberOfReferences()
          Deprecated. Returns the number of bibliographic references in a review article, or the empty (zero length) string if none was provided.
 OtherAbstract[] otherAbstracts()
          Deprecated. See class documentation.
 OtherID[] otherIDs()
          Deprecated. See class documentation.
 String owner()
          Deprecated. The owner is the group that created and validated this citation.
 PersonalNameSubject[] personalNameSubjects()
          Deprecated. See class documentation.
 String pmid()
          Deprecated. Returns the PubMed identifier for this document.
 String[] spaceFlightMissions()
          Deprecated. Returns a list of space flight names or mission numbers for articles on research carried out in space.
 String status()
          Deprecated. Returns the status of this citation.
 String toString()
          Deprecated. Returns a string-based representation of this citation.
 String xmlString()
          Deprecated. 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()
Deprecated. 
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()
Deprecated. 
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 DescriptionNotes
NLMNLM_VALUE (U.S.) National Library of Medicine, Index Section Value for majority of citations
NASANASA_VALUE (U.S.) National Aeronautics and Space Administration  
PIPPIP_VALUE Population Information Program, Johns Hopkins Not current; only on older citations
KIEKIE_VALUE Kennedy Institute of Ethics, Georgetown University  
HSRHSR_VALUE (U.S.) National Infomration Center on Health Services Reserach and Health Care Technology, National Library of Medicine  
HMDHMD_VALUE History of Medicine Division, National Library of Medicine  
SISSIS_VALUE Specialized Information Services Division, National Library of Medicine Not yet used; reserved for future use.
NOTNLMNOT_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()
Deprecated. 
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-ReviewIN_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-ProcessIN_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
CompletedCOMPLETED_VALUE These are 'true' MEDLINE records with date completed and typically with MeSH headings. This status remains under revisions.
PubMed-not-MEDLINEPUBMED_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.
PublisherPUBLISHER_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.
MEDLINEMEDLINE_VALUE 2005 addition not yet documented by the NLM.
OLDMEDLINEMEDLINE_VALUE 2005 addition not yet documented by the NLM.

Returns:
The status of this citation.

nlmDcmsID

public String nlmDcmsID()
Deprecated. 
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()
Deprecated. 
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()
Deprecated. 
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()
Deprecated. 
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()
Deprecated. 
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

@Deprecated
public Article article()
Deprecated. See class documentation.

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

Returns:
The article for this citation.

journalInfo

@Deprecated
public JournalInfo journalInfo()
Deprecated. See class documentation.

Returns information about the journal in which this citation appears.

Returns:
Information about the journal in which this citation appears.

chemicals

@Deprecated
public Chemical[] chemicals()
Deprecated. See class documentation.

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()
Deprecated. 
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

@Deprecated
public CommentOrCorrection[] commentOrCorrections()
Deprecated. See class documentation.

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

Returns:
The comments or corrections for this citaiton.

geneSymbols

public String[] geneSymbols()
Deprecated. 
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

@Deprecated
public MeshHeading[] meshHeadings()
Deprecated. See class documentation.

Returns an array of MeSH headings for this citation.

Returns:
An array of MeSH headings for this citation.

numberOfReferences

public String numberOfReferences()
Deprecated. 
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

@Deprecated
public PersonalNameSubject[] personalNameSubjects()
Deprecated. See class documentation.

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

@Deprecated
public OtherID[] otherIDs()
Deprecated. See class documentation.

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

@Deprecated
public OtherAbstract[] otherAbstracts()
Deprecated. See class documentation.

Returns the array of other abstracts for this citation.

Returns:
The array of other abstracts for this citation.

keywordLists

@Deprecated
public KeywordList[] keywordLists()
Deprecated. See class documentation.

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()
Deprecated. 
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

@Deprecated
public Investigator[] investigators()
Deprecated. See class documentation.

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

@Deprecated
public GeneralNote[] generalNotes()
Deprecated. See class documentation.

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()
Deprecated. 
Returns a string-based representation of this citation.

Overrides:
toString in class Object
Returns:
A string-based representation of this citation.