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README
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ofxPubmed
========
#Description
Library for request to Pubmed. Include example using a GUI for interact as advanced web mode.
This addon is created to get a Html response with the data requested from a personalized gui. This GUi has been created follwing the modus operanding from advanced Pubmed search.
Pubmed has many other tools of use. This add-on is just using eSearch tool. Manual steps for eSearch works properly, but anyway an advanced search bar (http://www.ncbi.nlm.nih.gov/pubmed/advanced) as modus operanding has been followed to it. And there is not official documentation for this, just the webside bar and logical request construction and the advanced name parameters.
The demo requires:
openFrameworks https://github.com/openframeworks/openFrameworks
ofxUI
ofxJson
ofxFTGL
Play clone add ons to get each personal addons (ofxUI its not the official)
#Use
Play the example (much esier) or used public methods to build your own request.
#License
xxx?
NLM leases the following data to U.S. and non-US individuals or organizations per the License Agreement at http://www.nlm.nih.gov/databases/license/license.pdf (printable version): MEDLINE/PubMed®
----
Technical Documentation......(very long sorry)
Types of search param:
[Alliation]
[All fields] // default
[Author]
[Author-Corporate]
[Author-First]
[Author - Full]
[Author - Identifier]
[Author - Last]
[Book]
[Date - Completion]
[Date - Create]
[Date - Entrez]
[Date - MeSH]
[Date - Modification]
[Date - Publication]
[EC/RN Number]
[Editor]
[Filter]
[Grant Number]
[ISBN]
[Investigator]
[Investigator - Full]
[Issue]
[Journal]
[Language]
[Location ID]
[MeSH Major Topic]
[MeSH Subheading]
[MeSH Subheading]
[Other Term]
[Pagination]
[Pharmacological Action]
[Publication Type]
[Publisher]
[Secondary Source ID]
[Supplementary Concept]
[Text Word]
[Title]
[Title/Abstract]
[Transliterated Title]
[Volume]
////////////////////////////////////////////////////////////////
//Manual: http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch
////////////////////////////////////////////////////////////////
INPUT
eutils/tool: Name of application making the E-utility call. Value must be a string with no internal spaces.
RESUME of tools:
EInfo DTD: eutils/einfo.fcgi
* Provides a list of the names of all valid Entrez databases.
* Provides statistics for a single database, including lists of indexing fields and available link names.
ESearch DTD: eutils/esearch.fcgi
* Provides a list of UIDs matching a text query
* Posts the results of a search on the History server
* Downloads all UIDs from a dataset stored on the History server
* Combines or limits UID datasets stored on the History server
* Sorts sets of UIDs
EPost DTD: eutils/epost.fcgi
* Uploads a list
ESummary DTD: eutils/esummary.fcgi
* Returns docs
EFetch: eutils/efetch.fcgi
* Returns formatted data records
ELink DTD: eutils/elink.fcgi
* Returns UIDs links..
EGQuery DTD: eutils/egquery.fcgi
* Provides the number of records retrieved in all Entrez databases by a single text query.
Ecitmatch: eutils/ecitmatch.cgi
* Retrieves PubMed IDs (PMIDs) that correspond to a set of input citation strings.
ESpell DTD (Retrieves PubMed IDs (PMIDs))
////////////////////////////////////////////////////////////////
//SEARCHING PARAMS
* ESearch: Base URL http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi
Functions:
- Provides a list of UIDs matching a text query
- Posts the results of a search on the History server
- Downloads all UIDs from a dataset stored on the History server
- Combines or limits UID datasets stored on the History server
- Sorts sets of UIDs
//Required Parameters
db: Database to search. Value must be a valid Entrez database name (default = pubmed).
term: Entrez text query. All special characters must be URL encoded. Spaces may be replaced by '+' signs. For very long queries (more than several hundred characters long), consider using an HTTP POST call. See the PubMed or Entrez help for information about search field descriptions and tags. Search fields and tags are database specific.
//Optional Parameters – [ History Server ]
(NIY)usehistory: When usehistory is set to 'y' (NIY = Not implemented yet)
(NIY)WebEnv: Web environment string returned from a previous ESearch (NIY)
(NIY)query_key:Integer query key returned by a previous ESearch, EPost or ELink call. When provided, ESearch will find the intersection of the set specified by query_key and the set retrieved by the query in term (i.e. joins the two with AND).For query_key to function, WebEnv must be assigned an existing WebEnv string and usehistory must be set to 'y'.
//Optional Parameters – [ Retrieval ]
//Optional Parameters – [ Dates ]
Datetype: Type of date used to limit a search. The allowed values vary between Entrez databases, but common values are 'mdat' (modification date), 'pdat' (publication date) and 'edat' (Entrez date). Generally an Entrez database will have only two allowed values for datetype.
reldate: When reldate is set to an integer n, the search returns only those items that have a date specified by datetype within the last n days.
mindate, maxdate: Date range used to limit a search result by the date specified by datetype. These two parameters (mindate, maxdate) must be used together to specify an arbitrary date range. The general date format is YYYY/MM/DD, and these variants are also allowed: YYYY, YYYY/MM.
-----------------------------------
Basic Searching
-----------------------------------
esearch.fcgi?db=<database>&term=<query>
Example: Get the PubMed IDs (PMIDs) for articles about breast cancer published in Science in 2008
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=science[journal]+AND+breast+cancer+AND+2008[pdat]
-----------------------------------
Optional Parameters – History Server
-----------------------------------
usehistory:
ESearch will post the UIDs resulting from the search operation onto the History server
Set to 'y'
WebEnv:
Web environment string returned from a previous ESearch
Set to 'y'
>> esearch.fcgi?db=pubmed&term=asthma&WebEnv=<webenv string>&usehistory=y
*** query_key: ***
Integer query key returned by a previous ESearch, EPost or ELink call. When provided, ESearch will find the intersection of the set specified by query_key and the set retrieved by the query in term (i.e. joins the two with AND). For query_key to function, WebEnv must be assigned an existing WebEnv string and usehistory must be set to 'y'.
Values for query keys may also be provided in term if they are preceeded by a '#' (%23 in the URL). While only one query_key parameter can be provided to ESearch, any number of query keys can be combined in term. Also, if query keys are provided in term, they can be combined with OR or NOT in addition to AND.
The following two URLs are functionally equivalent:
esearch.fcgi?db=pubmed&term=asthma&query_key=1&WebEnv=
<webenv string>&usehistory=y
esearch.fcgi?db=pubmed&term=%231+AND+asthma&WebEnv=
<webenv string>&usehistory=y
-----------------------------------
Optional Parameters – Retrieval
-----------------------------------
retmax:
Total number of UIDs from the retrieved set to be shown in the XML output (default = 20)
field:
If used, the entire search term will be limited to the specified Entrez field
>> esearch.fcgi?db=pubmed&term=asthma&field=title
>> esearch.fcgi?db=pubmed&term=asthma[title]
-----------------------------------
Optional Parameters – Dates
-----------------------------------
datetype:
Type of date used to limit a search.
common values are 'mdat' (modification date), 'pdat' (publication date) and 'edat' (Entrez date)
reldate:
When reldate is set to an integer n, the search returns only those items that have a date specified by datetype within the last n days.
mindate, maxdate:
Date range used to limit a search result
Examples:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=cancer&reldate=60&datetype=edat&retmax=100&usehistory=y
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=PNAS[ta]+AND+97[vi]&retstart=6&retmax=6&tool=biomed3
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nlmcatalog&term=obstetrics+AND+ncbijournals[filter]
-----------------------------------
Searching PubMed with Citation Data
-----------------------------------
ecitmatch.cgi?db=pubmed&rettype=xml&bdata=<citations>
Input: List of citation strings separated by a carriage return (%0D)
Example: Search PubMed for the following ciations:
Art1: Mann, BJ. (1991) Proc. Natl. Acad. Sci. USA. 88:3248
Art2: Palmenberg, AC. (1987) Science 235:182
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/ecitmatch.cgi?db=pubmed&retmode=xml&bdata=proc+natl+acad+sci+u+s+a|1991|88|3248|mann+bj|Art1|%0Dscience|1987|235|182|palmenberg+ac|Art2|
*/
////////////////////////////////////////////////////////////////
//Following abreviations can be usefull for determinated tools // not used
/*
PUBMED ELEMENTS ( Field Abbreviation )
From: http://www.nlm.nih.gov/bsd/mms/medlineelements.html
Abstract (AB)
Copyright Information (CI)
Affiliation (AD)
Investigator Affiliation (IRAD)
Article Identifier (AID)
Author (AU)
Author Identifier (AUID)
Full Author (FAU)
Book Title (BTI)
Collection Title (CTI)
Comments/Corrections
Corporate Author (CN)
Create Date (CRDT)
Date Completed (DCOM)
Date Created (DA)
Date Last Revised (LR)
Date of Electronic Publication (DEP)
Date of Publication (DP)
Entrez Date (EDAT)
MeSH Date (MHDA)
Edition (EN)
Editor and Full Editor Name (ED) (FED)
Gene Symbol (GS)
General Note (GN)
Grant Number (GR)
Investigator Name and Full Investigator Name (IR) (FIR)
ISBN (ISBN)
ISSN (IS)
Issue (IP)
Journal Title Abbreviation (TA)
Journal Title (JT)
Language (LA)
Location Identifier (LID)
Manuscript Identifier (MID)
MeSH Terms(MH)
NLM Unique ID (JID)
Number of References (RF)
Other Abstract and Other Abstract Language (OAB)(OABL)
Other Copyright Information (OCI)
Other ID (OID)
Other Term (OT)
Other Term Owner (OTO)
Owner (OWN)
Field Abbreviation
Pagination (PG)
Personal Name as Subject(PS)
Full Personal Name as Subject (FPS)
Place of Publication (PL)
Publication History Status(PHST)
Publication Status(PST)
Publication Type(PT)
Publishing Model(PUBM)
PubMed Central Identifier (PMC)
PubMed Central Release (PMCR)
PubMed Unique Identifier (PMID)
Registry Number/EC Number (RN)
Substance Name (NM)
Secondary Source ID (SI)
Source (SO)
Space Flight Mission (SFM)
Status (STAT)
Subset (SB)
Title (TI)
Transliterated Title (TT)
Volume (VI)
Volume Title (VTI)
*/
////////////////////////////////////////////////////////////////