package biocaml
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doc/biocaml.unix/Biocaml_unix/Entrez/index.html
Module Biocaml_unix.EntrezSource
Entrez Utilities API
This modules provides a partial access to Entrez databases such as Pubmed, Gene or Protein. The API proposed by the NCBI is based on HTTP requests, and this modules contains a couple of functions to ease the construction of appropriate URLs. This module also offers a more high-level access, with parsers for the answers from Entrez.
Databases in Entrez can be seen as collections of records, each record representing an object of the database. The basic usage of the low-level API is first to search a database with the esearch utility. Given a query string, esearch will return a collection of identifiers. These identifiers are then used to fetch the actual records with the efetch utility. These two operations are done in one call with the high-level API.
type database = [ | `gene| `genome| `geodatasets| `geoprofiles| `protein| `pubmed| `pubmedcentral| `sra| `unigene| `taxonomy
]Represents available databases
Low level access
For a documentation of the parameters, see this reference
val esearch_url :
?retstart:int ->
?retmax:int ->
?rettype:[ `uilist | `count ] ->
?field:string ->
?datetype:[ `pdat | `mdat | `edat ] ->
?reldate:int ->
?mindate:string ->
?maxdate:string ->
database ->
string ->
stringConstruction of esearch URLs.
Represents the result of a request to esearch
Parses an answer of esearch under XML format
Construction of esummary URLs
val efetch_url :
?rettype:string ->
?retmode:[ `xml | `text | `asn_1 ] ->
?retstart:int ->
?retmax:int ->
?strand:[ `plus | `minus ] ->
?seq_start:int ->
?seq_stop:int ->
database ->
string list ->
stringConstruction of efetch URLs. Note that this access method does not support more than 200 ids. For legible values of rettype and retmode please consult the official specification.