DAS registration

This page is part of the DAS 1.53E specification

Molecular interaction extension

Request: interaction command
Version: 2008/10/31
Authors: Hagen Blankenburg, Robert D. Finn, Andreas Prlic, Andrew Jenkinson, Mario Albrecht
Scope: DASMI Server
Command: interaction
Format:


PREFIX/das/DATASOURCE/interaction?interactor=ID
	[;interactor=ID]
	[;operation=INTERSECTION_UNION]
	[;detail=[ref:ID,]property:A_PROPERTY]
	[;detail=[ref:ID,]property:A_PROPERTY,value:A_VALUE]

Description: This section describes how a user or DAS client can request data from a DASMI server. The new DAS command for requesting interactions is named interaction and provides additional query parameters of three types, interactor, operation, and detail. The syntax of the interaction command is shown below.

Arguments: An interactor parameter represents an identifier of the target interactor. One or several interactor parameters can be provided. If only one interactor parameter is present, all available interaction partners of this interactor shall be returned.
The optional operation parameter can be used once for defining the response type if more than one interactor parameter is provided. If operation is not provided or has the value intersection, the interaction partners that interact with all query interactors shall be returned. If operation has the value union, the interactions for each of the query interactors shall be returned.
The detail parameter can be used to refine a query further. If the optional ref attribute is used, it indicates that the detail (e.g. an experimental role) is linked to the interactor with the same ID, if it is ommited the detail (e.g. a literature reference) is linked to the interation. A detail can be described in two different ways. The short form detail=property:A_PROPERTY will return all interactions for which the value of a certain property is present, regardless of what the value of that property is. In contrast, the long form detail=property:A_PROPERTY,value:A_VALUE will return all interactions for which a certain property is present and has a specific value. For example, while the short form allows for retrieving all interactions which possess a confidence score or a literature reference, the long form effects the retrieval of only those interactions for which that confidence score or literature reference has a specific value.
Examples:

.../das/DSN/interaction?interactor=3406

The simplest form of the interaction command is a request with exactly one interactor parameter. This query retrieves all interactions reported for the interactor with the Entrez Gene identifier 3406.

.../das/DSN/interaction?interactor=PF00121&detail=property:confidenceScore

This query returns all interactions reported for the domain interactor with the Pfam identifier PF00121, where a confidence score (regardless of the value of that score) has been assigned.

.../das/DSN/interaction?interactor=P38330

	&detail=ref:P38330,property:experimentalRole,value:bait

This query returns all interactions, where the protein interactor with the UniProt accession number P38330 has been used in the experimental role of a bait.

.../das/DSN/interaction?interactor=P52597&interactor=P60010

This query returns all interactions, where both protein interactors P52597 and P60010 are participating.

.../das/DSN/interaction?interactor=P52597&interactor=P60010

	&operation=UNION

Unlike the query above, this query returns all interactions, where either the protein interactor P52597 or the interactor P60010 are participating.

.../das/DSN/interaction?interactor=P38330;interactor=P32324;

	interactor=P10591;interactor=P16140

This exemplary query returns all protein complexes, where the four proteins P38330, P32324, P10591, and P16140 are participating.

.../interaction?interactor=P38330&interactor=P38332

	&detail=property:confidenceScore

	&detail=ref:P38330,property:experimentalRole,value:bait

	&detail=ref:P28332,property:experimentalRole,value:prey

This query would return all interactions, where the protein P38330 was used as a bait, P38332 was used as a prey, and a confidence score is available for the interaction.

Response: DASINT XML format This section defines the DASMI server response. The document returned from an interaction request is a DASINT XML document. Due to several optional elements and attributes, the complexity of the DASINT XML format may vary significantly.
Listing 1 shows the plainest possible form; Listing 2 shows the form fully utilizing all elements.
Listing 1: Plainest possible DASINT XML format.

<DASINT xmlns:xsi="xsd namespace" xmlns="namespace" 
	xsi:schemaLocation="schema location" >
	<INTERACTOR intId="id" shortLabel="name" dbSource="source" 
		dbAccessionId="acc" dbCoordSys="cs"/>
	<INTERACTION name="name" dbSource="source" dbAccessionId="acc">
		<PARTICIPANT intId="id"/>
		<PARTICIPANT intId="id"/>
	</INTERACTION>
</DASINT>

Listing 2: Completely utilized DASINT XML format.

<DASINT xmlns:xsi="xsd namespace" xmlns="namespace"
xsi:schemaLocation="schema location" >

<INTERACTOR intId="id" shortLabel="name" dbSource="source"
	dbSourceCvId="cv id" dbVersion="version"
	dbAccessionId="acc" dbCoordSys="cs">

	<DETAIL property="interactor property" value="a value"
		propertyCvId="cv id" valueCvId="cv id">
		<RANGE start="x" end="y" startStatus="status"
			endStatus="status" startStatusCvId="cv id"
			endStatusCvId="cv id"/>
	</DETAIL>

	<SEQUENCE start="x" end="y">SEQUENCESEQUENCE</SEQUENCE>

</INTERACTOR>

<INTERACTION name="name" dbSource="source" dbSourceCvId="cv id" 
	dbVersion="version" dbAccessionId="acc">

	<DETAIL property="interaction property" value="a value"
		propertyCvId="cv id" valueCvId="cvid">

		<PARTICIPANT intId="id">	
			<DETAIL property="participant property" value="a value"
					propertyCvId="cv id" valueCvId="cv id">
				<RANGE start="x" end="y" startStatus="status"
					endStatus="status" startStatusCvId="cv id"
					endStatusCvId="cv id"/>
			</DETAIL>
		</PARTICIPANT>

		<PARTICIPANT intId="id">
			<DETAIL property="participant property" value="a value"
				propertyCvId="cv id" valueCvId="cv id">
			<RANGE start="x" end="y" startStatus="status"
				endStatus="status" startStatusCvId="cv id"
				endStatusCvId="cv id"/>
			</DETAIL>
		</PARTICIPANT>
</INTERACTION>
</DASINT>

DASINT XML Schema Definition

An XML Schema defines the structure of an XML document, that is, the order, hierarchy, cardinality and type of its elements. An overview of the DASINT XML Schema Definition is shown in Figure 1.

Figure 1: DASINT XML Schema Definition.

Format:

<DASINT> (required; one)	The root element of the DASINT XML format is merely an outer envelope. The attribute xmlns:xsi indicates the official XML schema instance namespace. The attributes xmlns and xsi:schemaLocation define the DASINT namespace and the location of the DASINT XML Schema Definition, respectively.
<INTERACTOR> (required; one or more)	Each interactor, participating in an interaction, has to be initially defined within an INTERACTOR element. The INTERACTOR element thereby contains general, i.e., interaction independent, information on the interactor. The mandatory attributes shortLabel, dbSource, dbAccessionId and dbCoordSys define the origin and the identity of the interactor. The optional dbSourceCvId and dbVersion can be used to define the source database in more detail. The internal linkage between the interactor definition and its occurrence as a participant within an interaction is enabled with the intId attribute.
<INTERACTION> (required; one or more)	Being the central element within the DASINT protocol, each INTERACTION element represents one interaction. The mandatory attributes name, dbSource and dbAccessionId define the origin of the interaction. The optional dbSourceCvId and dbVersion can be used to further define the source database.
<PARTICIPANT> (required; two or more)	A participant is an interactor participating in an interaction. The participant can have additional, interaction dependent, features such as experimental role or binding sites. The linkage to the initial interactor definition is enabled through the sole attribute intId.
<SEQUENCE> (optional; zero or one per INTERACTOR)	The SEQUENCE element contains the sequence of the interactor. The type of the sequence, for instance, nucleotide or protein, is defined through the coordinate system of the interactor. The optional attributes start and end can be used to limit the sequence.
<DETAIL> (optional; zero or more per INTERACTOR, PARTICIPANT or INTERACTION)	The DETAIL element is the central element for providing additional information for the interactor, its role as a participant or an interaction. Depending on the father element, the detail is assigned to either one of these. To allow the element to contain all kinds of information, the mandatory attribute combination property and value is defined. To further define the property and the value through controlled vocabularies, the optional attributes propertyCvId and valueCvId can be used in addition.
<RANGE> (optional; zero or more per DETAIL)	The optional RANGE element may be used to limit a DETAIL to a certain position on the sequence of an interactor. If it is used, the mandatory start and end attributes define the associated stretch of the sequence. The optional startStatus and endStatus can be used to define the respective position more detailed with terms like "less than" or "greater than". To define these terms with controlled vocabulary terms, the attributes startStatusCvId and endStatusCvId can be used. Since an interaction does not have a sequence, the RANGE element may only be used within DETAIL elements that are child elements of either the INTERACTOR or the PARTICIPANT element.

Examples
The two following listings show potential applications of the DASINT XML format. The former Listing 3 describes a domain-domain interaction between two Pfam domains. The only additional information, besides the pure interaction information, is a confidence score assigned to the INTERACTION element. The latter Listing 4 represents a protein-protein interaction between two UniProt proteins and is far more detailed. It provides additional information for the interactor in general, its role as a participant, and the interaction. Listing 3: DASINT XML representing a domain-domain interaction between two Pfam domains. As an additional detail, a confidence score has been assigned to the interaction.

<?xml version="1.0" encoding="UTF-8"?>

<DASINT xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
		xmlns="http://dasmi.de/"
		xsi:schemaLocation="http://dasmi.de/ http://dasmi.de/dasint.xsd" >

	<INTERACTOR intId="1" shortLabel="Clp N" dbSource="Pfam"
		dbSourceCvId="MI:0451" dbVersion="20"
		dbAccessionId="PF02861" dbCoordSys="Pfam,Protein Sequence"/>
		
	<INTERACTOR intId="2" shortLabel="AAA" dbSource="Pfam"
		dbSourceCvId="MI:0451" dbVersion="20"
		dbAccessionId="PF00004" dbCoordSys="Pfam,Protein Sequence"/>

	<INTERACTION name="AAA-Clp N" dbSource="ldsc" dbAccessionId="">
		<DETAIL property="confidenceScore" value="38.0376"/>
		<PARTICIPANT intId="1"/>
		<PARTICIPANT intId="2"/>
	</INTERACTION>

</DASINT>

Listing 4: DASINT XML representing a protein-protein interaction between two UniProt proteins. Several additional details have been assigned to the interactor, the participant, and the interaction. Note that the SEQUENCE has been stripped.

<?xml version="1.0" encoding="UTF-8"?>
<DASINT xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
		xmlns="http://dasmi.de/"
		xsi:schemaLocation="http://dasmi.de/ http://dasmi.de/dasint.xsd" >

	<INTERACTOR intId="1" shortLabel="exo1 human"
		dbSource="uniprotkb" dbSourceCvId="MI:0486"
		dbAccessionId="Q9UQ84" dbVersion="SP 26"
		dbCoordSys="UniProt,Protein Sequence">
		<DETAIL property="type" value="protein"
			valueCvId="MI:0326"/>
		<SEQUENCE start="1" end="846">MGIQGLLK[..]KPECIFQ</SEQUENCE>
	</INTERACTOR>

	<INTERACTOR intId="2" shortLabel="msh2 human"
		dbSource="uniprotkb" dbSourceCvId="MI:0486"
		dbAccessionId="P43246" dbVersion="SP 59"
		dbCoordSys="UniProt,Protein Sequence">
	
		<DETAIL property="type" value="protein"
			valueCvId="MI:0326"/>
		<SEQUENCE start="1" end="934">MAVQPKEQ[..]REVFKT</SEQUENCE>
	</INTERACTOR>

	<INTERACTION name="exo1-msh2" dbSource="mint"
		dbSourceCvId="MI:0471" dbAccessionId="MINT-16442"
		dbVersion="2006-04-14">
		<DETAIL property="type" propertyCvId="MI:0190"
			value="aggregation" valueCvId="MI:0191"/>
		<PARTICIPANT intId="1">
			<DETAIL property="bindingSite" propertyCvId="MI:0117"
				value="">
				<RANGE start="604" end="846"/>
			</DETAIL>

			<DETAIL property="experimentalRole"
				propertyCvId="MI:0495" value="bait"
				valueCvId="MI:0496"/>
		</PARTICIPANT>

		<PARTICIPANT intId="2">
			<DETAIL property="bindingSite" propertyCvId="MI:0117"
				value="">
				<RANGE start="601" end="671"/>
			</DETAIL>
			<DETAIL property="experimentalRole"
				propertyCvId="MI:0495" value="prey"
				valueCvId="MI:0498"/>
		</PARTICIPANT>
	</INTERACTION>
</DASINT>

The DAS Registry^{V2.8.5 02 09 2010}

The Biological Distributed Annotation System Registry- Search (New Interface)

Molecular interaction extension

DASINT XML Schema Definition

The DAS RegistryV2.8.5 02 09 2010

The Biological Distributed Annotation System Registry- Search (New Interface)

Molecular interaction extension

DASINT XML Schema Definition

The DAS Registry^{V2.8.5 02 09 2010}