Module Biocaml.Entrez (.ml)

module Entrez: Biocaml_entrez

type database = [ `gene
       | `genome
       | `geodatasets
       | `geoprofiles
       | `protein
       | `pubmed
       | `pubmedcentral
       | `sra
       | `taxonomy
       | `unigene ]

Represents available databases

Low level access

For a documentation of the parameters, see this reference

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

Construction of esearch URLs.

type esearch_answer = {

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

}

Represents the result of a request to esearch

val esearch_answer_of_string : string -> esearch_answer

Parses an answer of esearch under XML format

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

Construction of esummary URLs

val efetch_url : ?rettype:string ->
       ?retmode:[ `asn_1 | `text | `xml ] ->
       ?retstart:int ->
       ?retmax:int ->
       ?strand:[ `minus | `plus ] ->
       ?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

module type Fetch = sig .. end

A signature for an HTTP request framework

module Make: functor (F : Fetch) -> sig .. end