Met­Ex­plore

Find­ing your path through net­work complexity

This is the online doc­u­men­ta­tion of the Met­Ex­plore Web Ser­vice v1.3

This web ser­vice allows users of the Met­Ex­plore web­site to pro­gram­mat­i­cally access their data. This doc­u­men­ta­tion can be found in .txt for­mat, at http://​met​ex​plore​.toulouse​.inra​.fr:8080/​m​e​t​E​x​p​l​o​r​e​W​e​b​S​e​r​v​i​c​e​/​d​o​c

Met­Ex­plore web­ser­vice is built using a REST­ful archi­tec­ture. All results will be given in a Json Format.

Imple­mented Functionalities:

Biosource Requests:


Our Web­Ser­vice allows users to retrieve the com­plete list of the net­works pub­licly avail­able on Met­Ex­plore. the rest of our web ser­vice uses inter­nal iden­ti­fiers for biosources. In order to find the cor­re­spond­ing id for a spe­cific net­work, use the following

http://​met​ex​plore​.toulouse​.inra​.fr:8080/​m​e​t​E​x​p​l​o​r​e​W​e​b​S​e​r​v​i​c​e​/​b​i​o​s​o​u​r​c​e​s

  • If you wish to find data on a sin­gle biosource throught our web ser­vice, use the following

http://metexplore.toulouse.inra.fr:8080/metExploreWebService/biosources/{YOURBIOSOURCEID}

Exam­ple: http://​met​ex​plore​.toulouse​.inra​.fr:8080/​m​e​t​E​x​p​l​o​r​e​W​e​b​S​e​r​v​i​c​e​/​b​i​o​s​o​u​r​c​e​s​/​1363

This will retrieve the spec­i­fied biosource from the pre­vi­ous list.

  • Retrieve the com­plete list of Bio enti­ties from a sin­gle net­work. The same syn­tax is used for each class of bio­log­i­cal entity

http://metexplore.toulouse.inra.fr:8080/metExploreWebService/biosources/{YOURBIOSOURCEID}/{Entity}

Accepted val­ues for the {Entity} para­me­ter are:

  • Com­part­ment
  • Path­way
  • Reac­tion
  • Metabo­lite
  • Enzyme
  • Pro­tein
  • Gene

For exam­ple, use :

http://​met​ex​plore​.toulouse​.inra​.fr:8080/​m​e​t​E​x​p​l​o​r​e​W​e​b​S​e​r​v​i​c​e​/​b​i​o​s​o​u​r​c​e​s​/​1363​/​M​e​t​a​b​o​l​i​t​e

To retrieve the full list of metabo­lites of the pub­lic net­work 1363, the Human metab­o­lism global recon­struc­tion Recon2.

  • Retrieve pre­cise data of a spe­cific entity in a par­tic­u­lar BioSource. This uses the unique id of the entity inside the scope of the net­work, it’s DBidentifier.

The same syn­tax is used for each class of Bio entity:

http://metexplore.toulouse.inra.fr:8080/metExploreWebService/biosources/{YOURBIOSOURCEID}/{Entity}/{Identifier}

Accepted val­ues for the {Entity} para­me­ter are:

  • Com­part­ment
  • Path­way
  • Reac­tion
  • Metabo­lite
  • Enzyme
  • Pro­tein
  • Gene

For exam­ple:

http://​met​ex​plore​.toulouse​.inra​.fr:8080/​m​e​t​E​x​p​l​o​r​e​W​e​b​S​e​r​v​i​c​e​/​b​i​o​s​o​u​r​c​e​s​/​1363​/​M​e​t​a​b​o​l​i​t​e​/​M​_​G​l​c​_​D​_​c

Will retrieve infor­ma­tion on the metabo­lite M_​Glc_​D_​c (D-​Glucose in this case) present in the pub­lic BioSource 1363, the Human metab­o­lism global recon­struc­tion, Recon2.


Link Requests:

This new fea­ture allow to link bio­log­i­cal enti­ties within a sin­gle biosource.

For exam­ple you can link metabo­lites and reactions:

http://​met​ex​plore​.toulouse​.inra​.fr:8080/​m​e​t​E​x​p​l​o​r​e​W​e​b​S​e​r​v​i​c​e​/​l​i​n​k​/​1363​/​r​e​a​c​t​i​o​n​s​/​m​e​t​a​b​o​l​i​t​e​s

This spe­cific request will also out­put the inter­ac­tion type of the reaction/​metabolite link:

{“idReaction”:“939201”,“idMetabolite”:“1107032”,“interaction”:“out”},
{“idReaction”:“939201”,“idMetabolite”:“1106903”,“interaction”:“in”}

in means the metabo­lites is an input of the reac­tion whereas out means the metabo­lite is an out­put of the reaction.

How­ever, if the reac­tion is reversible. Metabo­lites will be present twice as an in and an out interaction.

Note: Links requests are reversible, so

http://​met​ex​plore​.toulouse​.inra​.fr:8080/​m​e​t​E​x​p​l​o​r​e​W​e​b​S​e​r​v​i​c​e​/​l​i​n​k​/​1363​/​r​e​a​c​t​i​o​n​s​/​m​e​t​a​b​o​l​i​t​e​s

and

http://​met​ex​plore​.toulouse​.inra​.fr:8080/​m​e​t​E​x​p​l​o​r​e​W​e​b​S​e​r​v​i​c​e​/​l​i​n​k​/​1363​/​m​e​t​a​b​o​l​i​t​e​s​/​r​e​a​c​t​i​o​n​s

will out­put the same results.

Here is the list of avail­able link requests:

compartments/​metabolites
metabolites/​reactions
reactions/​enzymes
enzymes/​proteins
proteins/​genes

For inter­op­er­at­i­bil­ity between batabases we also added the fol­low­ing link request for metabolites

metabolites/​inchi
metabolites/​inchikey
metabolites/​chebi

Graph Requests:

This new fea­ture allows users to retrieve a given biosource in a Json­Graph for­mat. This for­mat can then be imported in our visu­al­i­sa­tion tool, Met­Ex­plore­Viz (doc­u­men­ta­tion here)


Here is an exam­ple of the full graph of the pub­lic net­work 1363, the Human metab­o­lism global recon­struc­tion Recon2:

http://​met​ex​plore​.toulouse​.inra​.fr:8080/​m​e​t​E​x​p​l​o​r​e​W​e​b​S​e​r​v​i​c​e​/​g​r​a​p​h​/​1363

Note: For large net­works, this request can take a few seconds.

The graph a user retrieves can be fil­tered upstream by one or sev­eral path­ways with this type of request:

http://​met​ex​plore​.toulouse​.inra​.fr:8080/​m​e​t​E​x​p​l​o​r​e​W​e​b​S​e​r​v​i​c​e​/​g​r​a​p​h​/​1363​/​f​i​l​t​e​r​e​d​b​y​p​a​t​h​w​a​y​?​p​a​t​h​w​a​y​i​d​l​i​s​t​=​(​123768​,​123735)

This will out­put the pre­vi­ous graph fil­tered by two pathways:

  • the “Chon­droitin syn­the­sis” path­way (id=123768)
  • the “Methio­n­ine and cys­teine metab­o­lism” path­way (id=123735)

The generic syn­tax is

pathwayidlist=(pathId1, pathId2,…, pathIdN)

The path­way ids can be retrieve by select­ing the “id” attrib­utes given by this webservice:

http://​met​ex​plore​.toulouse​.inra​.fr:8080/​m​e​t​E​x​p​l​o​r​e​W​e​b​S​e​r​v​i​c​e​/​b​i​o​s​o​u​r​c​e​s​/​1363​/​p​a​t​h​w​a​y​s


For bug reports or user-​specific requests please con­tact This email address is being pro­tected from spam­bots. You need JavaScript enabled to view it.