Difference between revisions of "iRefScape 0.8"

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<pre>
 
Date : 29th April 2010
 
  
The iRefIndex plugin for Cytoscape has been officially released.
+
This page describes the iRefScape 0.8 plug-in (specifically, iRefScape 0.89) for Cytoscape 2.6.3. See the following table for more detailed iRefScape compatibility information.
  
Join the Google groups e-mail list at http://groups.google.com/group/irefindex?hl=en
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{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"
to be informed of updates.
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! align="center" style="background:#f0f0f0;"|Cytoscape
 
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! align="center" style="background:#f0f0f0;"|iRefScape
The plugin works with both Cytoscape 2.6.3 and 2.7. However, nodes appear as circles (instead of as ellipses) in 2.7. 
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|-
A fix will be released for 2.7 shortly.
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| 2.7.0
</pre>
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| [[iRefScape 0.9]]
 +
|-
 +
| 2.6.3
 +
| iRefScape 0.8 (described on this page)
 +
|}
  
 +
Join the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group] to be informed of updates. See also the [[iRefScape|latest release of iRefScape]] which may differ from the release described here.
  
 
==Installation==
 
==Installation==
  
The plugin can be installed using Cytoscape's plugin menu. Select "Manage plugins" and then "Available for Install" and then "Network and Attribute I/O" and finally
+
The plugin can be installed using Cytoscape's plugin menu. Select "Manage plugins" and then "Available for Install" and then "Network and Attribute I/O" and finally '''"iRefScape v.0.8x"''' (where the precise version will use only digits, such as "iRefScape v.0.89").
  
'''iRefScape v.0.82'''. 
+
Follow the on-screen instructions.
  
Follow the on screen instructions.
+
More detailed instructions, troubleshooting tips and alternative methods are available on the [[iRefScape 0.8 Installation]] page.
  
More detailed instructions, trouble-shooting tips and alternative methods are available on the [http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.8x_Installation iRefIndex Cytoscape Plugin 0.8 installation page].
+
After, installation, select the entry of the form "iRefScape_0.8x" from Cytoscape's plugin menu.
  
After, installation, select '''iRefScape_0.82''' from Cytoscape's plugin menu.
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When the plugin is started for the first time, it will download the publicly available data set.
  
When the plugin is started for the first time, it will download the publicly available dataset.
+
== Using the Wizard - an example search ==
 
 
==Using the Wizard - an example search ==
 
  
 
Click the "Wizard" button - a pop-up window will appear.  
 
Click the "Wizard" button - a pop-up window will appear.  
Line 49: Line 50:
 
</gallery>
 
</gallery>
  
==Using the Search Panel==
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== Using the Search Panel ==
  
'''Enter query term(s)'''
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To perform a search, the following steps are involved:
  
Queries may be loaded from a file or by pasting the query into the text-box (one query per line).
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# Enter query term(s)
 +
# Select a search type
 +
# Select taxonomy/organism
 +
# Adjust search options (iterations, new view, canonical expansion) - this is optional
 +
# Start the search
  
'''Select a Search Type.''' 
+
=== Enter query term(s) ===
 +
 
 +
Queries may be loaded from a file or by pasting the query into the text box (one query per line). Multiple queries can also be separated by pipe characters (<tt>|</tt>) or by tab characters. Queries with spaces in them should be enclosed in double quotes.
 +
 
 +
=== Select a search type ===
  
 
Example searches are listed below.
 
Example searches are listed below.
  
{|class="wikitable" style="text-align:left" border="1" cellpadding="5"
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{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"
!width="50" align="center" style="background:#f0f0f0;"|Search Type
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! align="center" style="background:#f0f0f0;"|Search Type
!width="50" align="center" style="background:#f0f0f0;"|Example
+
! align="center" style="background:#f0f0f0;"|Example
!width="500" align="center" style="background:#f0f0f0;"|Notes
+
! align="center" style="background:#f0f0f0;"|Notes
 
|-
 
|-
| RefSeq_Ac||NP_996224||See http://www.ncbi.nlm.nih.gov/protein/221379660
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| <tt>RefSeq_Ac</tt>||<tt>NP_996224</tt>||See http://www.ncbi.nlm.nih.gov/protein/221379660
 
|-
 
|-
| UniProt_Ac||Q7KSF4||See http://www.uniprot.org/uniprot/Q7KSF4
+
| <tt>UniProt_Ac</tt>||<tt>Q7KSF4</tt>||See http://www.uniprot.org/uniprot/Q7KSF4
 
|-
 
|-
| UniProt_ID||Q7KSF4_DROME||See http://www.uniprot.org/uniprot/Q7KSF4
+
| <tt>UniProt_ID</tt>||<tt>Q7KSF4_DROME</tt>||See http://www.uniprot.org/uniprot/Q7KSF4
 
|-
 
|-
| geneID||42066||See http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=42066
+
| <tt>geneID</tt>||<tt>42066</tt>||See http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=42066
 
|-
 
|-
| geneSymbol||cher||See http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=42066
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| <tt>geneSymbol</tt>||<tt>cher</tt>||See http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=42066
 
|-
 
|-
| mass||72854<-->72866||Search protein interactors for a range of molecular mass (in Da).
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| <tt>mass</tt>||<tt>72854<-->72866</tt>||Search protein interactors for a range of molecular mass (in Da).
 
|-
 
|-
| rog||10121899||Redundant object group: iRefIndex's internal identifier for a protein
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| <tt>rog</tt>||<tt>10121899</tt>||Redundant object group: iRefIndex's internal identifier for a protein
 
|-
 
|-
| PMID||14605208||PubMed Identifier where an interaction is described.  See http://www.ncbi.nlm.nih.gov/pubmed
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| <tt>PMID</tt>||<tt>14605208</tt>||PubMed Identifier where an interaction is described.  See http://www.ncbi.nlm.nih.gov/pubmed.  Iterations and "Use canonical expansion" have no effect on this search type.  This search will return all protein interactors in the given PMID and will automatically draw all interactions known between these proteins (even if these interactions are supported by different PMIDs).  Select edges in the resulting graph, and see the i.PMID attribute in the Edge Attribute Browser.
 
|-
 
|-
| src_intxn_id||47513||Source interaction database identifier.   
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| <tt>src_intxn_id</tt>||<tt>EBI-212627</tt>||Source interaction database identifier.  Iterations and "Use canonical expansion" have no effect on this search type.  Caution: multiple databases may have overlapping interaction record identifiers (e.g. <tt>147805</tt> returns records from both BIND and BioGrid) and there is no way to limit this search to a specific database at this time.
 +
Equivalent interactions from other databases will be automatically retrieved using this search type (see provided example).
 
|-
 
|-
| omim||227650||OMIM identifier.  See http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=227650
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| <tt>omim</tt>||<tt>227650</tt>||OMIM identifier.  See http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=227650
 
|-
 
|-
| digid||449||Internal identifier for a group of phenotypically related diseases. See http://donaldson.uio.no/wiki/DiG:_Disease_groups
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| <tt>digid</tt>||<tt>449</tt>||Internal identifier for a group of phenotypically related diseases. See [[DiG: Disease groups]].  A digid can be found by first performing a search for some omim identifier - the digid will then appear as the i.digid node attribute.
 +
<!--
 
|-
 
|-
| dig_title||fanconi||Text search for a group of phenotypically related diseases. See http://donaldson.uio.no/wiki/DiG:_Disease_groups
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| <tt>dig_title</tt>||<tt>fanconi</tt>||Text search for a group of phenotypically related diseases. See [[DiG: Disease groups]]
 
|-
 
|-
 +
-->
 
|}
 
|}
  
'''Select a taxon or type in a taxon identifier.'''
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=== Select taxonomy/organism ===
 
    
 
    
This will limit the search results to this organism. See http://www.ncbi.nlm.nih.gov/taxonomy for more details on taxon identifiers. In most search types, it is ok to leave this set to "Any".
+
This will limit the search results to a particular organism. An organism can be selected from the list, or a taxonomy identifier can be entered into the field itself. See [http://www.ncbi.nlm.nih.gov/taxonomy Entrez Taxonomy] for more details on taxonomy identifiers. For most search types, it is acceptable to leave this field set to <tt>Any</tt>.
  
'''Choose a distance from the query list'''
+
=== Adjust search options ===
  
Selecting 0 will return only interactions between nodes found by the query list.
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The following optional adjustments can be made:
  
Selecting 1 will return immediate neighbours of nodes in the query list.
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==== Iterations ====
  
'''Expanded search'''
+
A distance from the query list's members can be specified:
  
Selecting the "Expand result using canonical mappings" will expand the search to include all proteins that are related to the query protein (for example, splice isoforms).  [See http://irefindex.uio.no/wiki/Canonicalization Canonicalization] for technical details.
+
* Selecting <tt>0</tt> will return only interactions between nodes found by the query list
 +
* Selecting <tt>1</tt> will return immediate neighbours of nodes in the query list
  
'''Press the "Search and load" button.'''
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==== Create new view ====
  
==Viewing the Results==
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A new view will be opened for the search results if this option is selected. Otherwise, the results will be added to the current view.
  
'''Colours and shapes'''
+
==== Use canonical expansion ====
  
# The blue node(s) corresponds to the protein found by your query.
+
Selecting this option will expand the search to include all proteins that are related to the query protein (for example, splice isoforms). See [http://irefindex.uio.no/wiki/Canonicalization Canonicalization] for technical details.
# Green nodes are interacting partners for your query protein.
 
# Purple hexagons are complex-nodes (also called pseudo-nodes). They keep partners of a complex together (i.e. QCR6_HUMAN is found in two complexes also involving “QCR2_HUMAN”).
 
# Orange-yellow edges indicate protein-protein interactions and pink edges represent membership of some protein in a complex.
 
  
'''Toggling edges'''
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=== Start the search ===
  
Multiple edges may appear between two nodes.  These represent separate interaction records that support this link.  Details on each original record can be viewed using the edge attribute viewer (below).  You can toggle this multi-view on and off by selecting "Toggle selected edges" in the iRefIndex menu.  Only one of the edges will be shown in the collapsed view.  
+
Press the "Search and load" button to perform the search.
  
'''Expanding your interaction map'''
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== Viewing the Results ==
  
You can search for additional interactions by right-clicking on a node and selecting "iRefIndex -- Retrieve interactions".
+
=== Colours and Shapes ===
  
Some example result displays are shown below.
+
* Blue nodes corresponds to proteins found by your query
 +
* Green nodes are interacting partners for your query protein
 +
* Purple hexagons are complex-nodes (also called pseudo-nodes); they keep partners of a complex together (i.e. QCR6_HUMAN is found in two complexes also involving "QCR2_HUMAN")
 +
* Orange-yellow edges indicate protein-protein interactions and pink edges represent membership of some protein in a complex
  
<gallery widths="500px" heights="300px">
+
=== Toggling Edges ===
Image:QCR2_HUMAN_initial.png|Results
 
Image:QCR2_HUMAN.png|Results (tidied)
 
</gallery>
 
  
+
Multiple edges may appear between two nodes.  These represent separate interaction records that support this link.  Details on each original record can be viewed using the edge attribute viewer (below).  You can toggle this multi-view on and off by selecting "Toggle selected multi-edges" in the iRefIndex/View Tools menu.  Only one of the edges will be shown in the collapsed view.
  
<!--
 
==Legend==
 
  
[[Image:Legand.jpg|500px|Legend]]
+
=== iRefScape Menu ===
 
-->
 
  
==Attributes==
+
The iRefScape menu in the CytoScape menu bar contains a number of other functions that may help with searching and viewing interaction data.  These are described in more detail on the [[iRefScape plugin menu]] page.
  
[[Image:Datapanel.jpg|thumb|500px|AtributeBrowser]]
+
=== Expanding the Interaction Map ===
  
 +
You can search for additional interactions by right-clicking on a node and selecting "iRefIndex -- Retrieve interactions".
  
There are two types of attributes available from iRefIndex: node attributes and edge attributes. These may be used to view information about selected nodes or edges (like i.taxid).  Some features may allow the user to link out to additional data sources through the "right-click" menu (like i.geneID). Features may also be used to sort and select nodes and edges with specific attributes (like i.order).  The i.query feature shows the user's query that is responsible for returning the node or edge.
+
Some example result displays are shown below.
  
Brief descriptions and examples of each attribute are provided below.  
+
<gallery widths="500px" heights="300px">
 +
Image:QCR2_HUMAN_initial.png|Results
 +
Image:QCR2_HUMAN.png|Results (tidied)
 +
</gallery>
  
#The user must first select the attributes that are to be displayed.
+
== Attributes ==
#This can be done by clicking on the "attribute" icon at the top of the node or edge attribute browser (red arrow).
 
  
 +
[[Image:iRefIndex-0.83-node-attributes-close-up-closed.png|right|The node attributes menu]]
  
 +
There are two types of attributes available from iRefIndex: node attributes and edge attributes. These may be used to view information about selected nodes or edges (like <tt>i.taxid</tt>).  Some features may allow the user to link out to additional data sources through the "right-click" menu (like <tt>i.geneID</tt>). Features may also be used to sort and select nodes and edges with specific attributes (like <tt>i.order</tt>). The <tt>i.query</tt> feature shows the user's query that is responsible for returning the node or edge.
  
 +
Brief descriptions and examples of each attribute are provided below.
  
 +
The user must first select the attributes that are to be displayed. This can be done by clicking on the "attribute" icon at the top of the node or edge attribute browser, as shown in the illustrative images.
  
 +
<div style="clear: right"></div>
 +
=== Node Attributes ===
  
===Node Attributes===
+
[[Image:iRefIndex-0.83-node-attributes-close-up-open.png|right|The open node attributes menu]]
  
Each node represents a distinct amino acid sequence (protein) from a distinct organism (taxon id).  Each of the attributes below, provide additional information about the node.  Although each node is distinct, a graph produced by iRefIndex may contain multiple nodes that are related proteins (i.e., splice isoform products from the same gene).  These nodes will all have the same "i.canonical_rog" and i.canonical_rogid" feature values.  See notes below.
+
Each node represents a distinct amino acid sequence (protein) from a distinct organism (taxonomy identifier).  Each of the attributes below, provide additional information about the node.  Although each node is distinct, a graph produced by iRefIndex may contain multiple nodes that are related proteins (such as splice isoform products from the same gene).  These nodes will all have the same <tt>i.canonical_rog</tt> and <tt>i.canonical_rogid</tt> feature values.  See the notes below.
  
Node attributes that can be lists of items (like i.UniProt) will have a corresponding attribute called i.[attribute name]_TOP (e.g. i.UniProt_TOP) that is the first item of the list.
+
Node attributes that can be lists of items (like <tt>i.UniProt</tt>) will have a corresponding attribute called <tt>i.''attribute name''_TOP</tt> (for example, <tt>i.UniProt_TOP</tt>) which provides the first item of the associated list.
  
 +
<div style="clear: right"></div>
  
{|class="wikitable" style="text-align:left" border="1" cellpadding="5"
+
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"
!width="50" align="center" style="background:#f0f0f0;"|Attribute name
+
! align="center" style="background:#f0f0f0;"|Attribute name
!width="50" align="center" style="background:#f0f0f0;"|Data type
+
! align="center" style="background:#f0f0f0;"|Data type
!width="50" align="center" style="background:#f0f0f0;"|Example value
+
! align="center" style="background:#f0f0f0;"|Example value
!width="400" align="center" style="background:#f0f0f0;"|Description
+
! align="center" style="background:#f0f0f0;"|Description
 
|-
 
|-
| ID||Integer||10121899||This is a unique identifier for the node assigned by iRefIndex (no two nodes will have the same ID). Each node corresponds to distinct amino acid sequence from a distinct taxon id.  See also i.rog and i.rogid
+
| <tt>ID</tt>||Integer||<tt>10121899</tt>||This is a unique identifier for the node assigned by iRefIndex (no two nodes will have the same ID). Each node corresponds to a distinct amino acid sequence from a distinct taxonomy identifier.  See also <tt>i.rog</tt> and <tt>i.rogid</tt>.
 
|-
 
|-
| canonicalName||Integer||10121899||This is the same as ID. This attribute is set by Cytoscape and is unrelated to the i.canonical_rog or i.canonical_rogid used by iRefIndex
+
| <tt>canonicalName</tt>||Integer||<tt>10121899</tt>||This is the same as <tt>ID</tt>. This attribute is set by Cytoscape and is unrelated to the <tt>i.canonical_rog</tt> or <tt>i.canonical_rogid</tt> used by iRefIndex
 
|-
 
|-
| i.RefSeq_Ac||List||[NP_996224] ||All RefSeq accessions with an amino acid sequence and taxon identifier identical to the protein represented by this node. Right click on this entry and select "Search [RefSeq_Ac] on the web -- Entrez -- Protein" for more information.  See also i.RefSeq_TOP for the first entry in this list of accessions.
+
| <tt>i.RefSeq_Ac</tt>||List||<tt>[NP_996224]</tt> ||All RefSeq accessions with an amino acid sequence and taxon identifier identical to the protein represented by this node. Right click on this entry and select "Search ''[RefSeq_Ac]'' on the web -- Entrez -- Protein" for more information.  See also <tt>i.RefSeq_TOP</tt> for the first entry in this list of accessions.
 
|-
 
|-
| i.UniProt_Ac||List||[Q7KSF4]||All UniProt accessions with an amino acid sequence and taxon identifier identical to the protein represented by this node. Right click on this entry and select "Search [UniProt_Ac] on the web -- UniProt -- KB Beta" for more information. See also i.UniProt_Ac_TOP for the first entry in this list of accessions.
+
| <tt>i.UniProt_Ac</tt>||List||<tt>[Q7KSF4]</tt>||All UniProt accessions with an amino acid sequence and taxonomy identifier identical to the protein represented by this node. Right click on this entry and select "Search ''[UniProt_Ac]'' on the web -- UniProt -- KB Beta" for more information. See also <tt>i.UniProt_Ac_TOP</tt> for the first entry in this list of accessions.
 
|-
 
|-
| i.UniProt_ID||List||[Q7KSF4_DROME] ||All UniProt IDs with an amino acid sequence and taxon identifier identical to the protein represented by this node. Right click on this entry and select "Search [UniProt_ID] on the web -- UniProt -- KB Beta" for more information. See also i.UniProt_ID_TOP for the first entry in this list of IDs.
+
| <tt>i.UniProt_ID</tt>||List||<tt>[Q7KSF4_DROME]</tt> ||All UniProt identifers with an amino acid sequence and taxonomy identifier identical to the protein represented by this node. Right click on this entry and select "Search ''[UniProt_ID]'' on the web -- UniProt -- KB Beta" for more information. See also <tt>i.UniProt_ID_TOP</tt> for the first entry in this list of IDs.
 
|-
 
|-
| i.canonical_rog||Integer||10121899||Related proteins (say splice isoforms from the same gene) will all belong to the same canonical group.  One member of this group is assigned as the canonical representative of this group.  The i.canonical_rog attribute lists the identifier of the protein's canonical group identifier.  For example, all products of Entrez Gene 42066 have the same i.canonical_rog (10121899).  Each of these gene products has its own identifier (because they each have a distinct amino acid sequence).  One of the splice isoforms (NP_996224) was chosen as the canonical representative of this group.  See http://irefindex.uio.no/wiki/Canonicalization for more details on how canonical groups are constructed and how canonical representatives are chosen.
+
| <tt>i.canonical_rog</tt>||Integer||<tt>10121899</tt>||Related proteins (say splice isoforms from the same gene) will all belong to the same canonical group.  One member of this group is assigned as the canonical representative of this group.  The <tt>i.canonical_rog</tt> attribute lists the identifier of the protein's canonical group identifier.  For example, all products of Entrez Gene 42066 have the same <tt>i.canonical_rog</tt> (<tt>10121899</tt>).  Each of these gene products has its own identifier (because they each have a distinct amino acid sequence).  One of the splice isoforms (<tt>NP_996224</tt>) was chosen as the canonical representative of this group.  See the [http://irefindex.uio.no/wiki/Canonicalization canonicalization document] for more details on how canonical groups are constructed and how canonical representatives are chosen.
 
|-
 
|-
| i.canonical_rogid||String||1ZFb1WlW0OgOlhiAPtkJTdb6oOg7227||This is a unique alphanumeric key for the canonical representative of the canonical group to which this node belongs. Briefly, an SHA-1 digest of the amino acid sequence is used to generate a unique 27 character key and this is pre-pended to the taxon id for the protein's source organism in order to make the rogid. See PMID 18823568 for details on how this key can be generated.    This is a string equivalent of the i.canonical_rog attribute. All canonical_rog's (an integer) have one corresponding canonical_rogid. See http://irefindex.uio.no/wiki/Canonicalization for more details on how canonical groups are constructed and how canonical representatives are chosen.  Note that the rogid for the protein represented by this specific node is listed under i.rogid.
+
| <tt>i.canonical_rogid</tt>||String||<tt>1ZFb1WlW0OgOlhiAPtkJTdb6oOg7227</tt>||This is a unique alphanumeric key for the canonical representative of the canonical group to which this node belongs. Briefly, an SHA-1 digest of the amino acid sequence is used to generate a unique 27 character key and this is prepended to the taxonomy identifier for the protein's source organism in order to make the rogid. See PMID 18823568 for details on how this key can be generated.    This is a string equivalent of the <tt>i.canonical_rog</tt> attribute. All <tt>i.canonical_rog</tt> instances (each being an integer) have one corresponding <tt>i.canonical_rogid</tt>. See the [http://irefindex.uio.no/wiki/Canonicalization canonicalization document] for more details on how canonical groups are constructed and how canonical representatives are chosen.  Note that the rogid for the protein represented by this specific node is listed under <tt>i.rogid</tt>.
 
|-
 
|-
| i.dataset||Integer||0||TO BE DESCRIBED
+
| <tt>i.dataset</tt>||Integer||<tt>0</tt>||'''TO BE DESCRIBED'''
 
|-
 
|-
| i.digid||List||449||This is an integer identifier that is shared by a group of disease entries in OMIM that are related by their titles.  See http://donaldson.uio.no/wiki/DiG:_Disease_groups for more details.  Also see i.omim and i.dig_title.
+
| <tt>i.digid</tt>||List||<tt>449</tt>||This is an integer identifier that is shared by a group of disease entries in OMIM that are related by their titles.  See [[DiG: Disease groups]] for more details.  Also see <tt>i.omim</tt> and <tt>i.dig_title</tt>.
 
|-
 
|-
| i.dig_title||List||[Fanconi anemia, complementation group B, 300514 (3), VACTERL association with hydrocephalus, X-linked, 314390 (3)]||These are entries from OMIM's Morbid Map that are all part of the same disease group.  See http://donaldson.uio.no/wiki/DiG:_Disease_groups for more details.  Also see i.omim and i.digid.
+
<!--
 +
| <tt>i.dig_title</tt>||List||<tt>[Fanconi anemia, complementation group B, 300514 (3), VACTERL association with hydrocephalus, X-linked, 314390 (3)]</tt>||These are entries from OMIM's Morbid Map that are all part of the same disease group.  See the [http://donaldson.uio.no/wiki/DiG:_Disease_groups disease groups document] for more details.  Also see <tt>i.omim</tt> and <tt>i.digid</tt>.
 +
-->
 
|-
 
|-
| i.displayLabel||List||[Q7KSF4_DROME] ||This is a list of short labels chosen by iRefIndex to label the node using the VizMapper. The UniProt ID is preferentially chosen (if one is available) followed by the Entrez Gene Symbol.  See also i.displayLabel_TOP for the first entry in this list.
+
| <tt>i.displayLabel</tt>||List||<tt>[Q7KSF4_DROME]</tt> ||This is a list of short labels chosen by iRefIndex to label the node using the VizMapper. The UniProt identifier is preferentially chosen (if one is available) followed by the Entrez Gene Symbol.  See also <tt>i.displayLabel_TOP</tt> for the first entry in this list.
 
|-
 
|-
| i.geneID||List||[42066]||All NCBI Entrez Gene Identifiers that encode a protein sequence identical to that of this node.  Right click on this entry and select "Search [geneID] on the web -- Entrez -- Gene" for more information.  See also i.geneID_TOP for the first entry in this list.
+
| <tt>i.geneID</tt>||List||<tt>[42066]</tt>||All NCBI Entrez Gene identifiers that encode a protein sequence identical to that of this node.  Right click on this entry and select "Search ''[geneID]'' on the web -- Entrez -- Gene" for more information.  See also <tt>i.geneID_TOP</tt> for the first entry in this list.
 
|-
 
|-
| i.geneSymbol||List||[CHER]||All NCBI Entrez Gene Official Sybols that encode a protein sequence identical to that of this node.  Right click on this entry and select "Search [geneSymbol] on the web -- Entrez -- Gene" for more information. See also i.geneSymbol_TOP for the first entry in this list.
+
| <tt>i.geneSymbol</tt>||List||<tt>[CHER]</tt>||All NCBI Entrez Gene official symbols that encode a protein sequence identical to that of this node.  Right click on this entry and select "Search ''[geneSymbol]'' on the web -- Entrez -- Gene" for more information. See also <tt>i.geneSymbol_TOP</tt> for the first entry in this list.
 
|-
 
|-
| i.interactor_description||List||[Q7KSF4_DROME, CHER, DMEL_CG3937, SKO, DMEL CG3937, FLN, CG3937, CHER, DMEL\\CG3937, FLN, SKO, CHER, NAME=CHER, DMEL_CG3937]||A collection of all the names in their short form as given by the original interaction databases.  See also i.interactor_description_TOP for the first entry in this list.
+
| <tt>i.interactor_description</tt>||List||<tt>[Q7KSF4_DROME, CHER, DMEL_CG3937, SKO, DMEL CG3937, FLN, CG3937, CHER, DMEL\\CG3937, FLN, SKO, CHER, NAME=CHER, DMEL_CG3937]</tt>||A collection of all the names in their short form as given by the original interaction databases.  See also <tt>i.interactor_description_TOP</tt> for the first entry in this list.
 
|-
 
|-
| i.mw||Integer|| 259142 ||Molecular weight associated with the protein sequence for this node.  From UniProt if available. You can search for nodes inside a MW range using the "mw" search type in the iRefIndex plugin.
+
| <tt>i.mass</tt>||Integer|| <tt>259142</tt> ||Mass associated with the protein sequence for this node.  From UniProt, if available. You can search for nodes inside a mass range using the <tt>mass</tt> search type in the iRefIndex plugin.
 
|-
 
|-
| i.omim||List||[608053]||List of OMIM disease identifiers associated with this protein.  Right click on the entry ans select Search for [omim] on the web -- Entrez -- OMIM for more information.  
+
| <tt>i.omim</tt>||List||<tt>[608053]</tt>||List of OMIM disease identifiers associated with this protein.  Right click on the entry and select "Search for ''[omim]'' on the web -- Entrez -- OMIM" for more information.  
 
|-
 
|-
| i.order||Integer|| 0 ||TO BE DESCRIBED. The distance of this node from the query node (query node = 0 , direct neighbors = 1 ). Pseudonodes have negative values (-1 = complex holder, -2 = collapsed instance )
+
| <tt>i.order</tt>||Integer|| <tt>0</tt> || The distance of this node from the query node (query node has distance <tt>0</tt>, nodes that are returned by a query because they are a part of the same canonical group have a value of <tt>10</tt>,  direct neighbours have a value of<tt>1</tt>). Pseudonodes have negative values (<tt>-1</tt> is a complex holder, <tt>-2</tt> is a collapsed instance).
 
|-
 
|-
| i.overall_degree||Integer|| 42 ||The total number of interactions described for this node in the iRefIndex database. Not all of these edges will be necessarily shown in the current view.  
+
| <tt>i.overall_degree</tt>||Integer|| <tt>42</tt> ||The total number of interactions described for this node in the iRefIndex database. Not all of these edges will be necessarily shown in the current view.  
 
|-
 
|-
| i.popularity||List|| 42 || TO BE DESCRIBED  
+
| <tt>i.popularity</tt>||List|| <tt>42</tt> || '''TO BE DESCRIBED'''
 
|-
 
|-
| i.pseudonode||Boolean|| false || This is set to true is the node represents a "complex" or n-ary interaction record. Protein nodes with edges incident to a pseudonode are member interactors from the interaction record where specific interactions between pairs of interactors is unknown.  Pseudonodes appear as hexagons when using the iRefIndex VizMapper style.  
+
| <tt>i.pseudonode</tt>||Boolean|| <tt>false</tt> || This is set to true is the node represents a "complex" or n-ary interaction record. Protein nodes with edges incident to a pseudonode are member interactors from the interaction record where specific interactions between pairs of interactors is unknown.  Pseudonodes appear as hexagons when using the iRefIndex VizMapper style.  
 
|-
 
|-
| i.query||String||NP_996224||The user query used to retrieve this specific node.  Neighbours of "query" nodes will not have an i.query value.  Nodes returned by queries are coloured blue when using the iRefIndex VizMapper style.
+
| <tt>i.query</tt>||String||<tt>NP_996224</tt>||The user query used to retrieve this specific node.  Neighbours of "query" nodes will not have an <tt>i.query</tt> value.  Nodes returned by queries are coloured blue when using the iRefIndex VizMapper style.
 
|-
 
|-
| i.rog||Integer||10121899||This is a unique identifier for the node assigned by iRefIndex (no two nodes will have the same ID). Each node corresponds to distinct amino acid sequence from a distinct taxon id. i.rog also appears as the ID attribute.  Each i.rog has a corresponding i.rogid - see below.
+
| <tt>i.rog</tt>||Integer||<tt>10121899</tt>||This is a unique identifier for the node assigned by iRefIndex (no two nodes will have the same ID). Each node corresponds to a distinct amino acid sequence associated with a distinct taxonomy identifier. <tt>i.rog</tt> also appears as the <tt>ID</tt> attribute.  Each <tt>i.rog</tt> has a corresponding <tt>i.rogid</tt> - see below.
 
|-
 
|-
| i.rogid||String||2mL9oLZ9g/SSPyK0nOz97RmOzPg3702||This is a unique alphanumeric key for the protein represented by this node. Briefly, an SHA-1 digest of the amino acid sequence is used to generate a unique 27 character key and this is pre-pended to the taxon id for the protein's source organism in order to make the rogid. See PMID 18823568 for details on how this key can be generated.    This is a string equivalent of the i.rog attribute. All i.rog's (an integer) have one corresponding i.rogid.
+
| <tt>i.rogid</tt>||String||<tt>2mL9oLZ9g/SSPyK0nOz97RmOzPg3702</tt>||This is a unique alphanumeric key for the protein represented by this node. Briefly, an SHA-1 digest of the amino acid sequence is used to generate a unique 27 character key and this is prepended to the taxonomy identifier for the protein's source organism in order to make the rogid. See PMID 18823568 for details on how this key can be generated.    This is a string equivalent of the <tt>i.rog</tt> attribute. All <tt>i.rog</tt> instances (each being an integer) have one corresponding <tt>i.rogid</tt>.
 
|-
 
|-
| i.taxid||Integer||7227||The NCBI taxonomy identifier for this protein's source organism.  See http://www.ncbi.nlm.nih.gov/taxonomy?term=7227 for more details.
+
| <tt>i.taxid</tt>||Integer||<tt>7227</tt>||The NCBI taxonomy identifier for this protein's source organism.  See http://www.ncbi.nlm.nih.gov/taxonomy?term=7227 for more details of this example value for <tt>i.taxid</tt>.
 
|-
 
|-
| i.xref||List||[AAF70826.1,Q9M6R5] ||All the accessions as given by the original interaction database records to describe this protein.  See also i.xref_TOP for the first entry in this list.
+
| <tt>i.xref</tt>||List||<tt>[AAF70826.1,Q9M6R5]</tt> ||All the accessions as given by the original interaction database records to describe this protein.  See also <tt>i.xref_TOP</tt> for the first entry in this list.
 
|-
 
|-
 
|}
 
|}
Line 226: Line 244:
  
  
{|class="wikitable" style="text-align:left" border="1" cellpadding="5"
+
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"
!width="50" align="center" style="background:#f0f0f0;"|Attribute name
+
! align="center" style="background:#f0f0f0;"|Attribute name
!width="50" align="center" style="background:#f0f0f0;"|Data type
+
! align="center" style="background:#f0f0f0;"|Data type
!width="50" align="center" style="background:#f0f0f0;"|Example value
+
! align="center" style="background:#f0f0f0;"|Example value
!width="400" align="center" style="background:#f0f0f0;"|Description
+
! align="center" style="background:#f0f0f0;"|Description
 
|-
 
|-
| ID||String||10121899 (2771704(40952)) 13911416||This is a unique identifier for the edge assigned by Cytoscape (no two edges would have same ID). See i.rig and i.rigid for unique identifiers for the edge assigned by iRefIndex.
+
| <tt>ID</tt>||String||<tt>10121899 (2771704(40952)) 13911416</tt>||This is a unique identifier for the edge assigned by Cytoscape (no two edges will have same <tt>ID</tt>). See <tt>i.rig</tt> and <tt>i.rigid</tt> for unique identifiers for the edge assigned by iRefIndex.
 
|-
 
|-
| i.PMID||Integer||14605208||Publication identifier of the publication where the interaction represented by the edge mentioned.  Right click on this entry and select: Search [PMID] on the web -- Entrez -- Pubmed for more details on the publication.
+
| <tt>i.PMID</tt>||Integer||<tt>14605208</tt>||Publication identifier of the publication where the interaction represented by the edge mentioned.  Right click on this entry and select "Search ''[PMID]'' on the web -- Entrez -- Pubmed" for more details on the publication.
 
|-
 
|-
| i.bait||Integer||13911416||Node ID for the protein that was used as a bait in this experiment.  Only applicable where the experimental system (see i.method_name) used to support this relationship was a bait-prey system (e.g. two hybrid).
+
| <tt>i.bait</tt>||Integer||<tt>13911416</tt>||Node ID for the protein that was used as a bait in this experiment.  Only applicable where the experimental system (see <tt>i.method_name</tt>) used to support this relationship was a bait-prey system (for example, two hybrid).
 
|-
 
|-
| i.canonical_rig||Integer||27799||See notes for i.rig edge feature.  This is the rig constructed for the interaction using its canonical rogs.  Use a web browser to query http://wodaklab.org/iRefWeb/interaction/show/27799 (where 27799 is the canonical_rig) to retrieve more information on this interaction and equivalent source interaction records.
+
| <tt>i.canonical_rig</tt>||Integer||<tt>27799</tt>||See notes for the <tt>i.rig</tt> edge feature.  This is the rig constructed for the interaction using its canonical rogs.  Use a web browser to query http://wodaklab.org/iRefWeb/interaction/show/27799 (where <tt>27799</tt> is the <tt>i.canonical_rig</tt> value) to retrieve more information on this interaction and equivalent source interaction records.
 
|-
 
|-
| i.experiment||String||Giot L [2003]||A short label for the experiment where this interaction was found (usually contains authors names).
+
| <tt>i.experiment</tt>||String||<tt>Giot L [2003]</tt>||A short label for the experiment where this interaction was found (usually contains authors names).
 
|-
 
|-
| i.flag||Integer||1||Used by iRefIndex plugin to control display of edges (0- the representative edge, used in edge toggle, 1- an edge which will disappear during edge toggle, 2- complex holder edge,6-a path7-Edge from or to a collapsed node).
+
| <tt>i.flag</tt>||Integer||<tt>1</tt>||Used by iRefIndex plugin to control display of edges (<tt>0</tt> being the representative edge, used in edge toggle; <tt>1</tt> being an edge which will disappear during edge toggle; <tt>2</tt> being a complex holder edge; <tt>6</tt> being a path; <tt>7</tt> being an edge from or to a collapsed node).
 
|-
 
|-
| i.host_taxid||Integer||7227||Indicates the organism taxon id where the interaction was experimentally demonstrated.
+
| <tt>i.host_taxid</tt>||Integer||<tt>7227</tt>||Indicates the organism taxonomy identifier where the interaction was experimentally demonstrated.
 
|-
 
|-
| i.isLoop||Integer||1||Indicates whether the interaction is a self interaction (i.e dimer or possibly multimer of the same protein type).  See the source interaction record for details.
+
| <tt>i.isLoop</tt>||Integer||<tt>1</tt>||Indicates whether the interaction is a self interaction (such as a dimer or possibly multimer of the same protein type).  See the source interaction record for details.
 
|-
 
|-
| i.method_cv||String||MI:0018||PSI-MI controlled vocabulary term id for the method used to provide evidence for this interaction.  See http://www.ebi.ac.uk/ontology-lookup/ for more details.  The name of the method is also given in the i.method_name feature.
+
| <tt>i.method_cv</tt>||String||<tt>MI:0018</tt>||PSI-MI controlled vocabulary term identifier for the method used to provide evidence for this interaction.  See http://www.ebi.ac.uk/ontology-lookup/ for more details.  The name of the method is also given in the <tt>i.method_name</tt> feature.
 
|-
 
|-
| i.method_name||String||two hybrid||PSI-MI controlled vocabulary term name for the method used to provide evidence for this interaction.  See http://www.ebi.ac.uk/ontology-lookup/ for more details.  The term identifer is also given in the i.method_cv feature.
+
| <tt>i.method_name</tt>||String||<tt>two hybrid</tt>||PSI-MI controlled vocabulary term name for the method used to provide evidence for this interaction.  See http://www.ebi.ac.uk/ontology-lookup/ for more details.  The term identifer is also given in the <tt>i.method_cv</tt> feature.
 
|-
 
|-
| i.participant_identification||String||predetermined participant||PSI-MI controlled vocabulary term for the participant identification method used to provide evidence for this interaction.  See http://www.ebi.ac.uk/ontology-lookup/ for more details.  The identifier for the term is also given in the i.participant_cv feature.
+
| <tt>i.participant_identification</tt>||String||<tt>predetermined participant</tt>||PSI-MI controlled vocabulary term for the participant identification method used to provide evidence for this interaction.  See http://www.ebi.ac.uk/ontology-lookup/ for more details.  The identifier for the term is also given in the <tt>i.participant_cv</tt> feature.
 
|-
 
|-
| i.participant_cv||String||predetermined participant||PSI-MI controlled vocabulary term id for the participant identification method used to provide evidence for this interaction.  See http://www.ebi.ac.uk/ontology-lookup/ for more details.  The term itself is also given in the i.participant_identification feature.
+
| <tt>i.participant_cv</tt>||String||<tt>predetermined participant</tt>||PSI-MI controlled vocabulary term identifier for the participant identification method used to provide evidence for this interaction.  See http://www.ebi.ac.uk/ontology-lookup/ for more details.  The term itself is also given in the <tt>i.participant_identification</tt> feature.
 
|-
 
|-
| i.type_cv||String||MI:0407||PSI-MI controlled vocabulary term id for the interaction type that occurs between the two proteins.  See http://www.ebi.ac.uk/ontology-lookup/ for more details.  The term itself is also given in the i.type_name feature.
+
| <tt>i.query</tt>||String||<tt>NP_996224</tt>||The user's query that is responsible for returning this edge.
 
|-
 
|-
| i.type_name||String||direct interaction||PSI-MI controlled vocabulary term id for the interaction type that occurs between the two proteins. See http://www.ebi.ac.uk/ontology-lookup/ for more detailsThe term itself is also given in the i.type_name feature.
+
| <tt>i.rig</tt>||Integer||<tt>27799</tt>||Redundant interaction group identifier for the interaction.  
 +
This is an integer equivalent of <tt>i.rigid</tt>Every rig has one corresponding rigid.
 
|-
 
|-
| i.query||String||NP_996224||The user's query that is responsible for returning this edge.
+
| <tt>i.rigid</tt>||String||<tt>TAabV6yJ1XzUvEhYwZLpu5reBU0</tt>||Redundant interaction group identifier for the interaction.  This is a universal key generated for the interaction by ordering according to ASCII value and concatentating the rogids participating in the interaction and then generating a Base-64 representation of an SHA-1 digest of the resulting string.  See PMID 18823568 for details on how this key can be generated.
 
|-
 
|-
| i.rig||Integer||27799||Redundant interaction group identifier for the interaction. This is an integer equivalent of the i.rigid. Every rig has one corresponding rigid.
+
| <tt>i.score_hpr</tt>||Integer||<tt>15</tt>||The hpr score (highest pmid re-use) is the highest number of interactions that any one PMID (supporting this interaction) is used to support.  See PMID 18823568 for details. See also <tt>i.score_np</tt> and <tt>i.score_lpr</tt>.
 
|-
 
|-
| i.rigid||String||TAabV6yJ1XzUvEhYwZLpu5reBU0||Redundant interaction group identifier for the interaction. This is a universal key generated for the interaction by asciibetically ordering and concatentating the rogids participating in the interaction and then generating a Base-64 representation of an SHA-1 digest of the resulting string.  See PMID 18823568 for details on how this key can be generated.
+
| <tt>i.score_lpr</tt>||Integer||<tt>11</tt>||The lpr score (lowest pmid re-use) is the lowest number of distinct interactions that any one PMID (supporting this interaction) is used to support. An lpr of greater than 20 is considered to be a high-throughput experiment.  See PMID 18823568 for details. See also <tt>i.score_np</tt> and <tt>i.score_lpr</tt>.
 
|-
 
|-
| i.score_hpr||Integer||15||The hpr score (highest pmid re-use) is the highest number of interactions that any one PMID (supporting this interaction) is used to support.  See PMID 18823568 for details. See also score_np and score_lpr.
+
| <tt>i.score_np</tt>||Integer||<tt>2</tt>||Number of PubMed Identifiers (PMIDs) pointing to literature where this interaction is supported.  See PMID 18823568 for details. See also <tt>i.score_lpr</tt>.
 
|-
 
|-
| i.score_lpr||Integer||11||The lpr score (lowest pmid re-use) is the lowest number of distinct interactions that any one PMID (supporting this interaction) is used to support. An lpr of greater than 20 is considered to be a high-throughput experiment.  See PMID 18823568 for details. See also score_np and score_lpr.
+
| <tt>i.source_protein</tt>||Integer||<tt>-1</tt>||'''TO BE DESCRIBED'''
 
|-
 
|-
| i.np||Integer||2||Number of PubMed Identifiers (PMIDs) pointing to literature where this interaction is supported.  See PMID 18823568 for details. See also score_np and score_lpr.
+
| <tt>i.src_intxn_db</tt>||String||<tt>grid</tt>||Original interaction database where this interaction record was obtained.
 
|-
 
|-
| i.source_protein||Integer||-1||TO BE DESCRIBED
+
| <tt>i.src_intxn_id</tt>||String||<tt>38677</tt>||Original interaction database where this interaction record was obtained. 
 +
In some case, it may be possible to right click and "Search ''[src_intxn_id]'' on the web -- Interaction databases -- the database" to see the original record.
 
|-
 
|-
| i.src_intxn_db||String||grid||Original interaction database where this interaction record was obtained.
+
| <tt>i.type_cv</tt>||String||<tt>MI:0407</tt>||PSI-MI controlled vocabulary term identifier for the interaction type that occurs between the two proteins.  See http://www.ebi.ac.uk/ontology-lookup/ for more details.  The term itself is also given in the <tt>i.type_name</tt> feature.
 
|-
 
|-
| i.src_intxn_id||String||38677||Original interaction database where this interaction record was obtained.   
+
| <tt>i.type_name</tt>||String||<tt>direct interaction</tt>||PSI-MI controlled vocabulary term identifier for the interaction type that occurs between the two proteinsSee http://www.ebi.ac.uk/ontology-lookup/ for more details.  The term itself is also given in the <tt>i.type_name</tt> feature.
In some case, it may be possible to right click and Search [src_intxn_id] on the web -- Interaction databases -- the database to see the original record.
 
 
|-
 
|-
| i.target_protein||Integer||-1||TO BE DESCRIBED
+
| <tt>i.target_protein</tt>||Integer||<tt>-1</tt>||'''TO BE DESCRIBED'''
 
|-
 
|-
 
|}
 
|}
  
 +
==Obtaining CORUM, DIP and HPRD Data==
  
==Obtaining HPRD and DIP data==
+
Due to licensing issues, we are unable to distribute these data with the plugin.  CORUM data and free IMex data from DIP will be included in the next public release of iRefIndex.
 
 
Due to licensing issues, we are unable to distribute HPRD and DIP data with the plugin.
 
  
 
You can request these data under a collaborative agreement by emailing ian.donaldson@biotek.uio.no
 
You can request these data under a collaborative agreement by emailing ian.donaldson@biotek.uio.no
Line 292: Line 310:
 
Under the agreement you agree to
 
Under the agreement you agree to
  
1. Not redistribute the data outside your research group.
+
# Not redistribute the data outside your research group.
 
+
# Provide us with feedback on your use of the data (problems and requests).
2. Provide us with feedback on your use of the data (problems and requests).
 
  
We do not require authorship on any related publications.
+
We do not require authorship on any related publications.
  
 +
==Obtaining Updates to the Data==
  
==Obtaining updates to the data==
+
You can check for and download updates to the dataset used by your plugin using the Wizard (see "Check for iRefIndex updates").
 
 
You can check for and download updates to the dataset used by your plugin using the Wizard (see Check for iRefIndex updates).
 
  
 
iRefIndex updates are announced through the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group]
 
iRefIndex updates are announced through the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group]
  
==Obtaining updates to the plugin==
+
==Obtaining Updates to the Plugin==
  
If you already have a plugin called iRefScape (a menu entry iRefScape_xx under the plugin menu of Cytoscape) and you want to make sure you have the latest version, use "Update plugins" from plugin menu. But, if you want to reinstall the plugin, you should uninstall previous versions of the plugin.  
+
If you already have a plugin called iRefScape (a menu entry "iRefScape" under the plugin menu of Cytoscape) and you want to make sure you have the latest version, use "Update plugins" from the "Plugins" menu. However, if you want to reinstall the plugin, you should uninstall any previous version of the plugin first.
  
 
Plugin updates are announced through the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group]
 
Plugin updates are announced through the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group]
Line 328: Line 344:
 
<p>[Sample batch file: [http://irefindex.uio.no/wikifiles//images/b/b1/Sample_batch_accessions.txt.zip]]</p>
 
<p>[Sample batch file: [http://irefindex.uio.no/wikifiles//images/b/b1/Sample_batch_accessions.txt.zip]]</p>
  
==Integrate user data to the plugin==
+
==Integrating User Data into the Plugin==
  
  
 
===How to create your own file to use as index===
 
===How to create your own file to use as index===
  
 
+
'''TO BE DESCRIBED'''
 
 
  
 
===How to create node and edge attributes ===
 
===How to create node and edge attributes ===
  
Example: Attaching disease group identifiers to Nodes (http://irefindex.uio.no/wiki/DiG:_Disease_groups)
+
Example: Attaching [http://irefindex.uio.no/wiki/DiG:_Disease_groups disease group] identifiers to nodes
 
 
 
 
 
 
  
 
==Updating==
 
==Updating==
Line 347: Line 359:
 
# Using plugins update feature
 
# Using plugins update feature
  
== Log files, search details and errors ==
+
== Log Files, Search Details and Errors ==
 
# How to interpret log messages and save them for later reference.  
 
# How to interpret log messages and save them for later reference.  
  
Line 355: Line 367:
  
  
== Exit plugin and force terminate operations  ==
+
== Exit plugin and force terminate operations  ==
 
The exit button performs two functions.  
 
The exit button performs two functions.  
 
# First one is to exit iRefIndex plugin, where the outcome is to detach the plugin from Cytoscape.  
 
# First one is to exit iRefIndex plugin, where the outcome is to detach the plugin from Cytoscape.  
Line 362: Line 374:
 
-->
 
-->
  
==Advanced path finding==
+
==Advanced Path-Finding==
 +
 
 +
[[Image:iRefIndex-0.83-path-original.png|thumb|500px|The path in the results, highlighted in green]]
 +
 
 +
iRefScape can be used to find interaction events connecting two proteins or a sequence of events involving several proteins.
  
iRefScape could be used to find interaction events connecting two proteins or a sequence of events involving several proteins.  
+
This process intakes two terminal nodes as input and returns all reasonable paths connecting these two. The results returned here are pathway independent. In other words, the sequences of interactions connecting the nodes are not constructed using currently published pathways. However, the paths returned may contain pathway centric information.
  
 +
The query format is as follows:
  
This process intakes two terminal nodes as input and returns all reasonable paths connecting these two. The results returned here are path way independent. i.e. the sequences of interactions connecting the nodes are not constructed using currently published pathways. However, the paths retuned may contain pathway centric information.
+
NP_004976 <==> NP_002871
  
The query format is :
+
Additional type and taxonomy parameters were also supplied as required:
NP_004976 <==> NP_002871 . additional type and taxon parameters were also supplied as required. (Type : RefSeq_AC, Taxon:9606).
 
This query located all reasonable paths between NP_004976 and NP_002871 and the returned path also contains the shortest path between them.
 
  
The results of the path finding was sorted in the ascending order of path length and the maximum path length was restricted by the “maximum_distance_allowed” variable with a default value of  6 (the value of this variable could be modified by changing the value of  “Maximum distance” from “Path Parameters tab” in advanced options). The paths found in this way were “reasonable paths”, this concept is different from finding the shortest path or finding all the paths. A “reasonable paths” path from A to B is a path extending from A to B where none of the intermediate  points can be reached from A with fewer steps by a path that extends from A via B (i.e when evaluating a path from A to B , nodes beyond B are not con-sidered).  Due to the way the algorithm works when the opposite search (NP_002871<==>NP_004976) was performed and it took 120 seconds and returned 3 paths. The reason behind this was that NP_002871 is directly connected to many hubs and therefore, initial seed-list size was larger than when stating with NP_004976.  The algorithm first try the direction requested by the user and after those considerers the opposite direction when creating the sub-network to look for path. The time consuming step in the NP_002871<==>NP_004976 was the initial evaluation step.  When constructing the query for path finding we used the attribute “i.overall_degree_TOP” and it provided the overall connectivity of the proteins within iRefIndex. The “i.overall_degree_TOP” value of RAF1 was 443 and for interested KRAS isoform was 2, therefore, although not shown in the graph RAF is connected to more than 400 other proteins than RAS1.  After the path finding was completed the “Path selection” panel can be used to selectively load the paths. In order to make the selection easier, the paths found can be represented by many attribute type and after conversion process the mouse over popup menu displays the path in selected attribute type.
+
* '''Search type:''' <tt>RefSeq_Ac</tt>
In the image below the green arrow show the path.
+
* '''Taxonomy:''' <tt>9606 (Homo sapiens)</tt>
  
<div >
+
This query located all reasonable paths between <tt>NP_004976</tt> and <tt>NP_002871</tt> and the returned path also contains the shortest path between them. The results of the path finding was sorted in the ascending order of path length and the maximum path length was restricted to a default value of 6; this value can be modified by changing the value of "Maximum distance" from the "Path parameters" tab in the advanced options panel. The paths found in this way were "reasonable paths", this concept is different from finding the shortest path or finding all the paths. A "reasonable path" from A to B is a path extending from A to B where none of the intermediate points can be reached from A with fewer steps by a path that extends from A via B (in other words, when evaluating a path from A to B, nodes beyond B are not considered).
<imagemap>
 
Image:Path NP 004976 NP 002871 copy.jpg|480x480px
 
default [http://www.biotek.uio.no]
 
</imagemap>
 
</div>
 
  
==Trouble shooting tips==
+
<div style="clear: right"></div>
* See http://cytoscape.org for a manual and a set of tutorials which describe the installation and use of Cytoscape.
+
=== Reversing the Path ===
  
* For problems with Cytoscape installation or use, try the [http://groups-beta.google.com/group/cytoscape-helpdesk Cytoscape Help Desk]  
+
[[Image:iRefIndex-0.83-path.png|thumb|500px|The path in the results, highlighted in green]]
 +
 
 +
Due to the way the algorithm works, when the opposite search was performed...
 +
 
 +
NP_002871 <==> NP_004976
 +
 
 +
...it took 120 seconds and returned 3 paths. The reason for this is that <tt>NP_002871</tt> is directly connected to many hubs and therefore, the initial seed-list size was larger than when starting with <tt>NP_004976</tt>. The algorithm first tries the direction requested by the user and after that considers the opposite direction when creating the sub-network to look for the path. The time consuming step in the opposite search (<tt>NP_002871<==>NP_004976</tt>) is thus the initial evaluation step. When constructing the query for path-finding we used the attribute <tt>i.overall_degree_TOP</tt> and it provided the overall connectivity of the proteins within iRefIndex. The <tt>i.overall_degree_TOP</tt> value of <tt>RAF1</tt> was found to be 443 and for the <tt>KRAS</tt> isoform was found to be 2. Therefore, although not shown in the graph, <tt>RAF</tt> is connected to more than 400 other proteins than <tt>RAS1</tt>.
 +
 
 +
In the image shown here, the green arrow shows the path.
 +
 
 +
<div style="clear: right"></div>
 +
=== Path Selection ===
 +
 
 +
[[Image:iRefIndex-0.83-path-selector.png|thumb|500px|The path selector for the results]]
 +
 
 +
After the path-finding is completed the "Path selection" panel can be used to selectively load the paths. In order to make the selection easier, the paths found can be described by a particular attribute type: by selecting a value from the list for "Convert pop-up type to" (such as <tt>RefSeq_Ac</tt>) and pressing the "Convert" button, a tooltip appearing over each path description will show the requested attribute values for each component of the path. Thus, a path description such as...
 +
 
 +
321631 -> 2229473 -> 4410739 -> 4531114
 +
 
 +
...will provide a tooltip showing the following identifiers:
  
* If you have problems with installation or use, please share your experience with us through the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group]
+
NP_002871 -> NP_001123914 -> NP_036979 -> NP_004976
  
*When updating data on Microsoft Windows XP and Vista. "Failed to find resources message" may appear in the log message window. If this happens please run the update again and the plugin will check and correct the problem during the second attempt.
+
==Troubleshooting==
  
 +
* See http://cytoscape.org/ for a manual and a set of tutorials which describe the installation and use of Cytoscape.
 +
* For problems with Cytoscape installation or use, try the [http://groups-beta.google.com/group/cytoscape-helpdesk Cytoscape Help Desk]
 +
* If you have problems with installation or use, please share your experience with us through the [http://groups.google.com/group/irefindex?hl=en iRefIndex Google Group]
 +
* When updating data on Microsoft Windows XP and Vista, a "Failed to find resources message" may appear in the log message window. If this happens please run the update again and the plugin will check and correct the problem during the second attempt.
 
* If you are working with large graphs, make sure Cytoscape has at least 128MB memory. See the following document for more information on setting up memory: http://cytoscape.org/cgi-bin/moin.cgi/How_to_increase_memory_for_Cytoscape
 
* If you are working with large graphs, make sure Cytoscape has at least 128MB memory. See the following document for more information on setting up memory: http://cytoscape.org/cgi-bin/moin.cgi/How_to_increase_memory_for_Cytoscape
  
Line 397: Line 430:
  
 
Follow this link for a listing of all iRefIndex related pages (archived and current).
 
Follow this link for a listing of all iRefIndex related pages (archived and current).
 +
 
[[Category:iRefIndex]]
 
[[Category:iRefIndex]]

Latest revision as of 16:18, 6 July 2011

Last edited: 2011-07-06

This page describes the iRefScape 0.8 plug-in (specifically, iRefScape 0.89) for Cytoscape 2.6.3. See the following table for more detailed iRefScape compatibility information.

Cytoscape iRefScape
2.7.0 iRefScape 0.9
2.6.3 iRefScape 0.8 (described on this page)

Join the iRefIndex Google Group to be informed of updates. See also the latest release of iRefScape which may differ from the release described here.

Installation

The plugin can be installed using Cytoscape's plugin menu. Select "Manage plugins" and then "Available for Install" and then "Network and Attribute I/O" and finally "iRefScape v.0.8x" (where the precise version will use only digits, such as "iRefScape v.0.89").

Follow the on-screen instructions.

More detailed instructions, troubleshooting tips and alternative methods are available on the iRefScape 0.8 Installation page.

After, installation, select the entry of the form "iRefScape_0.8x" from Cytoscape's plugin menu.

When the plugin is started for the first time, it will download the publicly available data set.

Using the Wizard - an example search

Click the "Wizard" button - a pop-up window will appear.

Follow these steps

  1. Select "Search protein-protein interactions for a protein".
  2. Select "UniProt identifier".
  3. For "Taxonomy identifier", select "9606 (Human)"
  4. Type QCR2_HUMAN in the provided space. Click "Next".
  5. Click "Search & load".

The images below show each of the steps in the wizard.

Using the Search Panel

To perform a search, the following steps are involved:

  1. Enter query term(s)
  2. Select a search type
  3. Select taxonomy/organism
  4. Adjust search options (iterations, new view, canonical expansion) - this is optional
  5. Start the search

Enter query term(s)

Queries may be loaded from a file or by pasting the query into the text box (one query per line). Multiple queries can also be separated by pipe characters (|) or by tab characters. Queries with spaces in them should be enclosed in double quotes.

Select a search type

Example searches are listed below.

Search Type Example Notes
RefSeq_Ac NP_996224 See http://www.ncbi.nlm.nih.gov/protein/221379660
UniProt_Ac Q7KSF4 See http://www.uniprot.org/uniprot/Q7KSF4
UniProt_ID Q7KSF4_DROME See http://www.uniprot.org/uniprot/Q7KSF4
geneID 42066 See http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=42066
geneSymbol cher See http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=42066
mass 72854<-->72866 Search protein interactors for a range of molecular mass (in Da).
rog 10121899 Redundant object group: iRefIndex's internal identifier for a protein
PMID 14605208 PubMed Identifier where an interaction is described. See http://www.ncbi.nlm.nih.gov/pubmed. Iterations and "Use canonical expansion" have no effect on this search type. This search will return all protein interactors in the given PMID and will automatically draw all interactions known between these proteins (even if these interactions are supported by different PMIDs). Select edges in the resulting graph, and see the i.PMID attribute in the Edge Attribute Browser.
src_intxn_id EBI-212627 Source interaction database identifier. Iterations and "Use canonical expansion" have no effect on this search type. Caution: multiple databases may have overlapping interaction record identifiers (e.g. 147805 returns records from both BIND and BioGrid) and there is no way to limit this search to a specific database at this time.

Equivalent interactions from other databases will be automatically retrieved using this search type (see provided example).

omim 227650 OMIM identifier. See http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=227650
digid 449 Internal identifier for a group of phenotypically related diseases. See DiG: Disease groups. A digid can be found by first performing a search for some omim identifier - the digid will then appear as the i.digid node attribute.

Select taxonomy/organism

This will limit the search results to a particular organism. An organism can be selected from the list, or a taxonomy identifier can be entered into the field itself. See Entrez Taxonomy for more details on taxonomy identifiers. For most search types, it is acceptable to leave this field set to Any.

Adjust search options

The following optional adjustments can be made:

Iterations

A distance from the query list's members can be specified:

  • Selecting 0 will return only interactions between nodes found by the query list
  • Selecting 1 will return immediate neighbours of nodes in the query list

Create new view

A new view will be opened for the search results if this option is selected. Otherwise, the results will be added to the current view.

Use canonical expansion

Selecting this option will expand the search to include all proteins that are related to the query protein (for example, splice isoforms). See Canonicalization for technical details.

Start the search

Press the "Search and load" button to perform the search.

Viewing the Results

Colours and Shapes

  • Blue nodes corresponds to proteins found by your query
  • Green nodes are interacting partners for your query protein
  • Purple hexagons are complex-nodes (also called pseudo-nodes); they keep partners of a complex together (i.e. QCR6_HUMAN is found in two complexes also involving "QCR2_HUMAN")
  • Orange-yellow edges indicate protein-protein interactions and pink edges represent membership of some protein in a complex

Toggling Edges

Multiple edges may appear between two nodes. These represent separate interaction records that support this link. Details on each original record can be viewed using the edge attribute viewer (below). You can toggle this multi-view on and off by selecting "Toggle selected multi-edges" in the iRefIndex/View Tools menu. Only one of the edges will be shown in the collapsed view.


iRefScape Menu

The iRefScape menu in the CytoScape menu bar contains a number of other functions that may help with searching and viewing interaction data. These are described in more detail on the iRefScape plugin menu page.

Expanding the Interaction Map

You can search for additional interactions by right-clicking on a node and selecting "iRefIndex -- Retrieve interactions".

Some example result displays are shown below.

Attributes

The node attributes menu

There are two types of attributes available from iRefIndex: node attributes and edge attributes. These may be used to view information about selected nodes or edges (like i.taxid). Some features may allow the user to link out to additional data sources through the "right-click" menu (like i.geneID). Features may also be used to sort and select nodes and edges with specific attributes (like i.order). The i.query feature shows the user's query that is responsible for returning the node or edge.

Brief descriptions and examples of each attribute are provided below.

The user must first select the attributes that are to be displayed. This can be done by clicking on the "attribute" icon at the top of the node or edge attribute browser, as shown in the illustrative images.

Node Attributes

The open node attributes menu

Each node represents a distinct amino acid sequence (protein) from a distinct organism (taxonomy identifier). Each of the attributes below, provide additional information about the node. Although each node is distinct, a graph produced by iRefIndex may contain multiple nodes that are related proteins (such as splice isoform products from the same gene). These nodes will all have the same i.canonical_rog and i.canonical_rogid feature values. See the notes below.

Node attributes that can be lists of items (like i.UniProt) will have a corresponding attribute called i.attribute name_TOP (for example, i.UniProt_TOP) which provides the first item of the associated list.

Attribute name Data type Example value Description
ID Integer 10121899 This is a unique identifier for the node assigned by iRefIndex (no two nodes will have the same ID). Each node corresponds to a distinct amino acid sequence from a distinct taxonomy identifier. See also i.rog and i.rogid.
canonicalName Integer 10121899 This is the same as ID. This attribute is set by Cytoscape and is unrelated to the i.canonical_rog or i.canonical_rogid used by iRefIndex
i.RefSeq_Ac List [NP_996224] All RefSeq accessions with an amino acid sequence and taxon identifier identical to the protein represented by this node. Right click on this entry and select "Search [RefSeq_Ac] on the web -- Entrez -- Protein" for more information. See also i.RefSeq_TOP for the first entry in this list of accessions.
i.UniProt_Ac List [Q7KSF4] All UniProt accessions with an amino acid sequence and taxonomy identifier identical to the protein represented by this node. Right click on this entry and select "Search [UniProt_Ac] on the web -- UniProt -- KB Beta" for more information. See also i.UniProt_Ac_TOP for the first entry in this list of accessions.
i.UniProt_ID List [Q7KSF4_DROME] All UniProt identifers with an amino acid sequence and taxonomy identifier identical to the protein represented by this node. Right click on this entry and select "Search [UniProt_ID] on the web -- UniProt -- KB Beta" for more information. See also i.UniProt_ID_TOP for the first entry in this list of IDs.
i.canonical_rog Integer 10121899 Related proteins (say splice isoforms from the same gene) will all belong to the same canonical group. One member of this group is assigned as the canonical representative of this group. The i.canonical_rog attribute lists the identifier of the protein's canonical group identifier. For example, all products of Entrez Gene 42066 have the same i.canonical_rog (10121899). Each of these gene products has its own identifier (because they each have a distinct amino acid sequence). One of the splice isoforms (NP_996224) was chosen as the canonical representative of this group. See the canonicalization document for more details on how canonical groups are constructed and how canonical representatives are chosen.
i.canonical_rogid String 1ZFb1WlW0OgOlhiAPtkJTdb6oOg7227 This is a unique alphanumeric key for the canonical representative of the canonical group to which this node belongs. Briefly, an SHA-1 digest of the amino acid sequence is used to generate a unique 27 character key and this is prepended to the taxonomy identifier for the protein's source organism in order to make the rogid. See PMID 18823568 for details on how this key can be generated. This is a string equivalent of the i.canonical_rog attribute. All i.canonical_rog instances (each being an integer) have one corresponding i.canonical_rogid. See the canonicalization document for more details on how canonical groups are constructed and how canonical representatives are chosen. Note that the rogid for the protein represented by this specific node is listed under i.rogid.
i.dataset Integer 0 TO BE DESCRIBED
i.digid List 449 This is an integer identifier that is shared by a group of disease entries in OMIM that are related by their titles. See DiG: Disease groups for more details. Also see i.omim and i.dig_title.
i.displayLabel List [Q7KSF4_DROME] This is a list of short labels chosen by iRefIndex to label the node using the VizMapper. The UniProt identifier is preferentially chosen (if one is available) followed by the Entrez Gene Symbol. See also i.displayLabel_TOP for the first entry in this list.
i.geneID List [42066] All NCBI Entrez Gene identifiers that encode a protein sequence identical to that of this node. Right click on this entry and select "Search [geneID] on the web -- Entrez -- Gene" for more information. See also i.geneID_TOP for the first entry in this list.
i.geneSymbol List [CHER] All NCBI Entrez Gene official symbols that encode a protein sequence identical to that of this node. Right click on this entry and select "Search [geneSymbol] on the web -- Entrez -- Gene" for more information. See also i.geneSymbol_TOP for the first entry in this list.
i.interactor_description List [Q7KSF4_DROME, CHER, DMEL_CG3937, SKO, DMEL CG3937, FLN, CG3937, CHER, DMEL\\CG3937, FLN, SKO, CHER, NAME=CHER, DMEL_CG3937] A collection of all the names in their short form as given by the original interaction databases. See also i.interactor_description_TOP for the first entry in this list.
i.mass Integer 259142 Mass associated with the protein sequence for this node. From UniProt, if available. You can search for nodes inside a mass range using the mass search type in the iRefIndex plugin.
i.omim List [608053] List of OMIM disease identifiers associated with this protein. Right click on the entry and select "Search for [omim] on the web -- Entrez -- OMIM" for more information.
i.order Integer 0 The distance of this node from the query node (query node has distance 0, nodes that are returned by a query because they are a part of the same canonical group have a value of 10, direct neighbours have a value of1). Pseudonodes have negative values (-1 is a complex holder, -2 is a collapsed instance).
i.overall_degree Integer 42 The total number of interactions described for this node in the iRefIndex database. Not all of these edges will be necessarily shown in the current view.
i.popularity List 42 TO BE DESCRIBED
i.pseudonode Boolean false This is set to true is the node represents a "complex" or n-ary interaction record. Protein nodes with edges incident to a pseudonode are member interactors from the interaction record where specific interactions between pairs of interactors is unknown. Pseudonodes appear as hexagons when using the iRefIndex VizMapper style.
i.query String NP_996224 The user query used to retrieve this specific node. Neighbours of "query" nodes will not have an i.query value. Nodes returned by queries are coloured blue when using the iRefIndex VizMapper style.
i.rog Integer 10121899 This is a unique identifier for the node assigned by iRefIndex (no two nodes will have the same ID). Each node corresponds to a distinct amino acid sequence associated with a distinct taxonomy identifier. i.rog also appears as the ID attribute. Each i.rog has a corresponding i.rogid - see below.
i.rogid String 2mL9oLZ9g/SSPyK0nOz97RmOzPg3702 This is a unique alphanumeric key for the protein represented by this node. Briefly, an SHA-1 digest of the amino acid sequence is used to generate a unique 27 character key and this is prepended to the taxonomy identifier for the protein's source organism in order to make the rogid. See PMID 18823568 for details on how this key can be generated. This is a string equivalent of the i.rog attribute. All i.rog instances (each being an integer) have one corresponding i.rogid.
i.taxid Integer 7227 The NCBI taxonomy identifier for this protein's source organism. See http://www.ncbi.nlm.nih.gov/taxonomy?term=7227 for more details of this example value for i.taxid.
i.xref List [AAF70826.1,Q9M6R5] All the accessions as given by the original interaction database records to describe this protein. See also i.xref_TOP for the first entry in this list.

Edge Attributes

Each edge represents a distinct primary database record that supports some relationship between the two incident nodes. So, if an interaction between two proteins has been annotated by two databases (or twice by the same database) then two edges will appear between those two protein nodes.


Attribute name Data type Example value Description
ID String 10121899 (2771704(40952)) 13911416 This is a unique identifier for the edge assigned by Cytoscape (no two edges will have same ID). See i.rig and i.rigid for unique identifiers for the edge assigned by iRefIndex.
i.PMID Integer 14605208 Publication identifier of the publication where the interaction represented by the edge mentioned. Right click on this entry and select "Search [PMID] on the web -- Entrez -- Pubmed" for more details on the publication.
i.bait Integer 13911416 Node ID for the protein that was used as a bait in this experiment. Only applicable where the experimental system (see i.method_name) used to support this relationship was a bait-prey system (for example, two hybrid).
i.canonical_rig Integer 27799 See notes for the i.rig edge feature. This is the rig constructed for the interaction using its canonical rogs. Use a web browser to query http://wodaklab.org/iRefWeb/interaction/show/27799 (where 27799 is the i.canonical_rig value) to retrieve more information on this interaction and equivalent source interaction records.
i.experiment String Giot L [2003] A short label for the experiment where this interaction was found (usually contains authors names).
i.flag Integer 1 Used by iRefIndex plugin to control display of edges (0 being the representative edge, used in edge toggle; 1 being an edge which will disappear during edge toggle; 2 being a complex holder edge; 6 being a path; 7 being an edge from or to a collapsed node).
i.host_taxid Integer 7227 Indicates the organism taxonomy identifier where the interaction was experimentally demonstrated.
i.isLoop Integer 1 Indicates whether the interaction is a self interaction (such as a dimer or possibly multimer of the same protein type). See the source interaction record for details.
i.method_cv String MI:0018 PSI-MI controlled vocabulary term identifier for the method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The name of the method is also given in the i.method_name feature.
i.method_name String two hybrid PSI-MI controlled vocabulary term name for the method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term identifer is also given in the i.method_cv feature.
i.participant_identification String predetermined participant PSI-MI controlled vocabulary term for the participant identification method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The identifier for the term is also given in the i.participant_cv feature.
i.participant_cv String predetermined participant PSI-MI controlled vocabulary term identifier for the participant identification method used to provide evidence for this interaction. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term itself is also given in the i.participant_identification feature.
i.query String NP_996224 The user's query that is responsible for returning this edge.
i.rig Integer 27799 Redundant interaction group identifier for the interaction.

This is an integer equivalent of i.rigid. Every rig has one corresponding rigid.

i.rigid String TAabV6yJ1XzUvEhYwZLpu5reBU0 Redundant interaction group identifier for the interaction. This is a universal key generated for the interaction by ordering according to ASCII value and concatentating the rogids participating in the interaction and then generating a Base-64 representation of an SHA-1 digest of the resulting string. See PMID 18823568 for details on how this key can be generated.
i.score_hpr Integer 15 The hpr score (highest pmid re-use) is the highest number of interactions that any one PMID (supporting this interaction) is used to support. See PMID 18823568 for details. See also i.score_np and i.score_lpr.
i.score_lpr Integer 11 The lpr score (lowest pmid re-use) is the lowest number of distinct interactions that any one PMID (supporting this interaction) is used to support. An lpr of greater than 20 is considered to be a high-throughput experiment. See PMID 18823568 for details. See also i.score_np and i.score_lpr.
i.score_np Integer 2 Number of PubMed Identifiers (PMIDs) pointing to literature where this interaction is supported. See PMID 18823568 for details. See also i.score_lpr.
i.source_protein Integer -1 TO BE DESCRIBED
i.src_intxn_db String grid Original interaction database where this interaction record was obtained.
i.src_intxn_id String 38677 Original interaction database where this interaction record was obtained.

In some case, it may be possible to right click and "Search [src_intxn_id] on the web -- Interaction databases -- the database" to see the original record.

i.type_cv String MI:0407 PSI-MI controlled vocabulary term identifier for the interaction type that occurs between the two proteins. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term itself is also given in the i.type_name feature.
i.type_name String direct interaction PSI-MI controlled vocabulary term identifier for the interaction type that occurs between the two proteins. See http://www.ebi.ac.uk/ontology-lookup/ for more details. The term itself is also given in the i.type_name feature.
i.target_protein Integer -1 TO BE DESCRIBED

Obtaining CORUM, DIP and HPRD Data

Due to licensing issues, we are unable to distribute these data with the plugin. CORUM data and free IMex data from DIP will be included in the next public release of iRefIndex.

You can request these data under a collaborative agreement by emailing ian.donaldson@biotek.uio.no

Under the agreement you agree to

  1. Not redistribute the data outside your research group.
  2. Provide us with feedback on your use of the data (problems and requests).

We do not require authorship on any related publications.

Obtaining Updates to the Data

You can check for and download updates to the dataset used by your plugin using the Wizard (see "Check for iRefIndex updates").

iRefIndex updates are announced through the iRefIndex Google Group

Obtaining Updates to the Plugin

If you already have a plugin called iRefScape (a menu entry "iRefScape" under the plugin menu of Cytoscape) and you want to make sure you have the latest version, use "Update plugins" from the "Plugins" menu. However, if you want to reinstall the plugin, you should uninstall any previous version of the plugin first.

Plugin updates are announced through the iRefIndex Google Group


Advanced Path-Finding

The path in the results, highlighted in green

iRefScape can be used to find interaction events connecting two proteins or a sequence of events involving several proteins.

This process intakes two terminal nodes as input and returns all reasonable paths connecting these two. The results returned here are pathway independent. In other words, the sequences of interactions connecting the nodes are not constructed using currently published pathways. However, the paths returned may contain pathway centric information.

The query format is as follows:

NP_004976 <==> NP_002871

Additional type and taxonomy parameters were also supplied as required:

  • Search type: RefSeq_Ac
  • Taxonomy: 9606 (Homo sapiens)

This query located all reasonable paths between NP_004976 and NP_002871 and the returned path also contains the shortest path between them. The results of the path finding was sorted in the ascending order of path length and the maximum path length was restricted to a default value of 6; this value can be modified by changing the value of "Maximum distance" from the "Path parameters" tab in the advanced options panel. The paths found in this way were "reasonable paths", this concept is different from finding the shortest path or finding all the paths. A "reasonable path" from A to B is a path extending from A to B where none of the intermediate points can be reached from A with fewer steps by a path that extends from A via B (in other words, when evaluating a path from A to B, nodes beyond B are not considered).

Reversing the Path

The path in the results, highlighted in green

Due to the way the algorithm works, when the opposite search was performed...

NP_002871 <==> NP_004976

...it took 120 seconds and returned 3 paths. The reason for this is that NP_002871 is directly connected to many hubs and therefore, the initial seed-list size was larger than when starting with NP_004976. The algorithm first tries the direction requested by the user and after that considers the opposite direction when creating the sub-network to look for the path. The time consuming step in the opposite search (NP_002871<==>NP_004976) is thus the initial evaluation step. When constructing the query for path-finding we used the attribute i.overall_degree_TOP and it provided the overall connectivity of the proteins within iRefIndex. The i.overall_degree_TOP value of RAF1 was found to be 443 and for the KRAS isoform was found to be 2. Therefore, although not shown in the graph, RAF is connected to more than 400 other proteins than RAS1.

In the image shown here, the green arrow shows the path.

Path Selection

The path selector for the results

After the path-finding is completed the "Path selection" panel can be used to selectively load the paths. In order to make the selection easier, the paths found can be described by a particular attribute type: by selecting a value from the list for "Convert pop-up type to" (such as RefSeq_Ac) and pressing the "Convert" button, a tooltip appearing over each path description will show the requested attribute values for each component of the path. Thus, a path description such as...

321631 -> 2229473 -> 4410739 -> 4531114

...will provide a tooltip showing the following identifiers:

NP_002871 -> NP_001123914 -> NP_036979 -> NP_004976

Troubleshooting

  • See http://cytoscape.org/ for a manual and a set of tutorials which describe the installation and use of Cytoscape.
  • For problems with Cytoscape installation or use, try the Cytoscape Help Desk
  • If you have problems with installation or use, please share your experience with us through the iRefIndex Google Group
  • When updating data on Microsoft Windows XP and Vista, a "Failed to find resources message" may appear in the log message window. If this happens please run the update again and the plugin will check and correct the problem during the second attempt.
  • If you are working with large graphs, make sure Cytoscape has at least 128MB memory. See the following document for more information on setting up memory: http://cytoscape.org/cgi-bin/moin.cgi/How_to_increase_memory_for_Cytoscape

All iRefIndex Pages

Follow this link for a listing of all iRefIndex related pages (archived and current).