Overview
In this page it is explained how to use the data contained in mentha either by plugging the interactome browser or by using mentha API. The graphical application can be embedded in your web-page and it can be fed with UniProt IDs. All the data contained in mentha can be accessed through REST interface. mentha will also offer drawing tools to represent interactions and pathway.

You can query mentha via PSICQUIC or via mentha's APIs, described below.
If you want to use PSICQUIC, here you can find how to implement your queries LINK
Example:
http://mentha.uniroma2.it:9090/psicquic/webservices/current/search/query/*?firstResult=0&maxResults=100


The following organisms are currently supported:
All set org=all
Homo sapiens set org=9606
Arabidopsis thaliana set org=3702
Caenorhabditis elegans set org=6239
Escherichia coli K12 set org=83333
Drosophila melanogaster set org=7227
Mus musculus set org=10090
Rattus norvegicus set org=10116
Saccharomyces cerevisiae set org=559292

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mentha developer's tools

RESTful API Interactome Browser Applet

mentha API


REST interface
In order to access the data archived in mentha you can use the following commands.

List of Servlets
The HOME for each method is http://mentha.uniroma2.it:8080/server/

METHOD	DESCRIPTION
getEvidence	This method returns all the evidence supporting the interaction between two proteins. ida: UniProt ID of the first protein idb: UniProt ID of the second protein org: Organism Example      HOME/getEvidence?org=9606&ida=O00273&idb=P63104 Result format      Interaction type ; Experimental method ; PMID ; Source database ; DOI
getInteractions	This method returns all the binary interactions in which one of the queried proteins is involved. ids: UniProt IDs separated by comma org: Organism Example      HOME/getInteractions?org=9606&ids=O00273,P63104 Result format      Protein A ; Protein B ; Score Example      HOME/getInteractions?org=all&ids=O00273,P63104 Result format      Protein A ; Organism A ; Protein B ; Organism B ; Score
isEnzymatic	This method returns 1 or 0 if the interaction between two proteins has evidence to be enzymatic. This result is inferred by using experimental methods and interaction types in order to see whether they may be used to describe enzymatic interactions, as formalised in OLS - Ontology Lookup Service. ida: UniProt ID of the first protein idb: UniProt ID of the second protein org: Organism Example      HOME/isEnzymatic?org=9606&ida=O00273&idb=P63104
doOnInteractome	This method is a powerful method that returns processed information. In specific, it is possible to compute paths and thus, selectively extract information. s: UniProt ID of the source protein t: UniProt ID od the target protein action: Algorithms  [minpath | allhops]. w: Consider weighted graph th: Set a threshold from 0 to 1 g: Return result as gene names org: Organism - warning: ALL is not allowed Examples In this example mentha will return one path with minimum number of steps (w=0, weights are ignored) that contains only edges with a score higher than 0.3. HOME/doOnInteractome?org=9606&action=minpath&s=O00273&t=P42226&th=0.3&g=1&w=0 In this example mentha will return one minimal path considering weights (w=1) that contains only edges with a score higher than 0.3. HOME/doOnInteractome?org=9606&action=minpath&s=O00273&t=P42226&th=0.3&g=1&w=1 In this example mentha will return all paths with minimum number of steps. HOME/doOnInteractome?org=9606&action=allhops&s=O00273&t=P42226&g=1

mentha Interactome Browser Applet If you want to embed the Graphical Application in your web-pages you have to create an <iframe> using the following line. http://mentha.uniroma2.it/browser/plug.html?org=all&ids=P05388,O95793&x=320&y=200 The following code is an example, and below it, you can see the result. <iframe     width="350px"     height="250px"     scrolling="no"     frameborder="0"     style="overflow: hidden;"     src="http://mentha.uniroma2.it/browser/plug.html?ids=P05388,O95793&x=320&y=240&org=all"> </iframe> Result

mentha Interactive Graph Drawer (mentha IGD) mentha IGD is a javascript library that allows you to draw interactions among proteins and/or other elements. mentha IGD is used by the Protein Bag to draw a preview of the network you are analysing. EXAMPLE If you want to create an image with mentha IGD you just have to add the following lines to your page: <div id="area" style="width:800px;height:600px;text-align:center;"></div> <script src="http://mentha.uniroma2.it/graphViewer/mentha-IGD.js"></script> The above lines will create an area of 800x600 pixels that will contain the drawing. var links = [ {source: "Protein 1", idA: "Q9GZZ7", typeA: "protein", target: "TSC2", idB: "P49815", typeB: "protein", type: "none", score: "0.5"}, {source: "Protein 2", idA: "Q7Z429", typeA: "protein", target: "TSC2", idB: "P49815", typeB: "protein", type: "none", score: "0.5"}]; the variable links will hold the network to visualise    - Source and Target are simply labels and can contain any text.    - idA and idB are the two Unirot protein ID (or any ID). Mandatory for all proteins.    - typeA and typeB at the moment it can be "protein", "complex", "chemical", "small molecule" (Are only graphical representation, no special feaures)    - type at the moment it can be "none", "activation", "inhibition" var edge_labels = new Array(); edge_labels["Q9GZZ7P49815"] = "Edge description"; The variable edge_labels will hold egdes(links) labels. The key in this associative array must be idAidB concatenated where the order counts. Text can be HTML. var node_labels = new Array(); node_labels["Q9GZZ7"] = "Node description"; The variable node_labels will hold nodes(circles) labels. The key in this associative array must be the id od an entity in your graph. Once you have your edges defined call: initGraph(links,node_labels,edge_labels,"area",300,300); Parameters 1) variable containing edges 2) nodes labels 3) edges labels 4) div that will contain the drawing 5,6) div size 7) Value 1 displays membrane and nucleus placing receptors and factors. Value 0 shows a floating graph