package biocaml

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in-package search v0.2.0

The OCaml Bioinformatics Library

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biocaml.org Readme Edit opam file Versions (5)

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B

biocaml@googlegroups.com

Sources

v0.11.0.tar.gz

md5=486aeb3e552dabae85839e2af30d6c52

sha512=4ed2df0b7cbd80bd6e29bd8fee9d2dacd9379ad0f4ff142bd8e16ade3f1507f6cc7cbe4c614943b8feb8fa4705935695cb458606b0da813dbf255b1e566a43cf

doc/biocaml.unix/Biocaml_unix/Entrez/index.html

Module `Biocaml_unix.Entrez`Source

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.

Sourcetype 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

Source

val esearch_url : 
  ?retstart:int ->
  ?retmax:int ->
  ?rettype:[ `uilist | `count ] ->
  ?field:string ->
  ?datetype:[ `pdat | `mdat | `edat ] ->
  ?reldate:int ->
  ?mindate:string ->
  ?maxdate:string ->
  database ->
  string ->
  string

Construction of esearch URLs.

Sourcetype esearch_answer = {

count : int;
retmax : int;
retstart : int;
ids : string list;

}

Represents the result of a request to esearch

Sourceval esearch_answer_of_string : string -> esearch_answer

Parses an answer of esearch under XML format

Source

val esummary_url : 
  ?retstart:int ->
  ?retmax:int ->
  database ->
  string list ->
  string

Construction of esummary URLs

Source

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 ->
  string

Construction 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.

High level access

Sourcemodule type Fetch = sig ... end

A signature for an HTTP request framework

Sourcemodule Make (F : Fetch) : sig ... end

On This Page

Low level access
High level access

package biocaml

Install

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Authors

Maintainers

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doc/biocaml.unix/Biocaml_unix/Entrez/index.html

Module Biocaml_unix.EntrezSource

Low level access

High level access

Module `Biocaml_unix.Entrez`Source