sig
type database =
[ `gene
| `genome
| `geodatasets
| `geoprofiles
| `protein
| `pubmed
| `pubmedcentral
| `sra
| `taxonomy
| `unigene ]
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
type esearch_answer =
Biocaml_entrez.esearch_answer = {
count : int;
retmax : int;
retstart : int;
ids : string list;
}
val esearch_answer_of_string : string -> esearch_answer
val esummary_url :
?retstart:int -> ?retmax:int -> database -> string list -> string
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
module type Fetch =
sig
type 'a fetched
val fetch : string -> (string -> 'a) -> 'a fetched
val ( >>= ) : 'a fetched -> ('a -> 'b fetched) -> 'b fetched
val ( >|= ) : 'a fetched -> ('a -> 'b) -> 'b fetched
end
module Make :
functor (F : Fetch) ->
sig
module Object_id :
sig
type t = [ `int of int | `string of string ]
val to_string : t -> string
end
module Dbtag :
sig
type t =
Biocaml_entrez.Make(F).Dbtag.t = {
db : string;
tag : Object_id.t;
}
end
module Gene_ref :
sig
type t =
Biocaml_entrez.Make(F).Gene_ref.t = {
locus : string option;
allele : string option;
desc : string option;
maploc : string option;
pseudo : bool option;
db : Dbtag.t list;
}
end
module PubmedSummary :
sig
type t =
Biocaml_entrez.Make(F).PubmedSummary.t = {
pmid : int;
doi : string option;
pubdate : string option;
source : string option;
title : string;
}
val search : string -> t list F.fetched
end
module Pubmed :
sig
type t =
Biocaml_entrez.Make(F).Pubmed.t = {
pmid : int;
title : string;
abstract : string;
}
val search : string -> t list F.fetched
end
module Gene :
sig
type t =
Biocaml_entrez.Make(F).Gene.t = {
_type :
[ `miscRNA
| `ncRNA
| `other
| `protein_coding
| `pseudo
| `rRNA
| `scRNA
| `snRNA
| `snoRNA
| `tRNA
| `transposon
| `unknown ];
summary : string option;
gene : Gene_ref.t;
}
val search : string -> t list F.fetched
end
end
end