Difference between revisions of "PSICQUIC Web Services for iRefIndex"
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| − | + | {{Note| | |
| − | + | Access the WebService | |
| + | The list of available services are available under https://irefindex.vib.be/webservices/ | ||
| + | }} | ||
| − | + | ||
| − | http:// | + | |
| + | These services provide programmatic access to iRefIndex data as well as many other interaction databases and are further described in a Nature Methods article [http://www.nature.com/nmeth/journal/v8/n7/full/nmeth.1637.html available here]. | ||
| + | |||
| + | These services are based on a template from the IntAct group at EBI that was developed and implemented by a consortium of authors and interaction database groups. | ||
| + | |||
| + | <pre> | ||
| + | A related interface called PSISCORE, provides programmatic access to interaction data scoring methods. | ||
| + | |||
| + | This interface is currently discontinued until a new location is arranged for it. | ||
| + | </pre> | ||
| + | |||
| + | "PSICQUIC" is pronounced like the English word "psychic" as in the ability to perceive information hidden from the normal senses through extrasensory perception. | ||
| + | |||
| + | A number of use cases are envisioned for these services. For example, once implemented by multiple interaction databases, they would allow a user to make a query for information at one database web-site and then have that query replicated at all other interaction databases (that have implemented the service interface). The user could then receive a compiled list of results that match their query regardless of the database that contains the information. | ||
| + | |||
| + | Note that only the first 15 columns of the iRefIndex MITAB files are returned from this service. The full data set is available via FTP download as described on the [[README_MITAB2.6_for_iRefIndex|iRefIndex MITAB page]] and via [http://wodaklab.org/iRefWeb/ iRefWeb]. | ||
| + | |||
| + | WSDL locations: | ||
| + | *http://irefindex.vib.be/psicquic/webservices/psicquic?wsdl | ||
| + | |||
| + | |||
| + | Version information: | ||
| + | *http://irefindex.vib.be/psicquic/webservices/psicquic/getVersion | ||
Available services: | Available services: | ||
| − | + | *https://irefindex.vib.be/webservices/ | |
| − | + | All active services: | |
| − | http://www.ebi.ac.uk/ | + | *http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS |
| + | REST service samples: | ||
| + | *http://irefindex.vib.be/psicquic/webservices/current/search/query/species:4932 | ||
| + | *http://irefindex.vib.be/psicquic/webservices/current/search/query/species:9606 | ||
| − | + | More details about the project: | |
| − | + | *http://code.google.com/p/psicquic/ | |
| − | |||
| + | IntAct PSICQUIC View: | ||
| + | *http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml | ||
| − | + | The format and content of the interaction data returned by these services is described on the [[README_MITAB2.6_for_iRefIndex]] page. | |
| + | ===Changes from last version=== | ||
| − | + | There are major changes between iRefindex PSICQUIC service version 1.1.5 and version 1.1.6. In 1.1.5 the results returned were interaction-centric (one line in the results representing one binary interaction or a complex membership). From 1.1.6 onwards the results will be experiment-centric (one line per evidence per source). The new extended PSI MI-TAB (version 2.6) is used in the implementation, but only the first 15 columns will be available at the moment in order to maintain compatibility with other services. For further details on the returned results please refer the [[README_MITAB2.6_for_iRefIndex]] page. | |
| − | + | The second major change is the usage of UniProt and RefSeq identifiers as uidA and uidB whenever that is possible. | |
Users are advised that there are differences between our implementation of these services and that of other databases. | Users are advised that there are differences between our implementation of these services and that of other databases. | ||
| − | Most notably, | + | Most notably, interactions between 3 or more proteins (n-ary data) are represented in the PSI-MITAB files using a bi-partite model (one of the first two columns is used to represent the complex and the second column is used to represent a member of the complex). Other PSICQUIC services will likely use a spoke model representation. |
| + | |||
| + | Please refer to our documentation above and documentation provided by other PSICQUIC providers if you plan to combine results from multiple services. | ||
| + | |||
| + | == Main iRefIndex Page == | ||
| − | + | http://irefindex.org/ | |
| − | + | == All iRefIndex Pages == | |
| − | + | Follow this link for a listing of all iRefIndex related pages (archived and current). | |
| + | [[Category:iRefIndex]] | ||
Latest revision as of 17:23, 28 December 2019
 Note |
Access the WebService The list of available services are available under https://irefindex.vib.be/webservices/ |
These services provide programmatic access to iRefIndex data as well as many other interaction databases and are further described in a Nature Methods article available here.
These services are based on a template from the IntAct group at EBI that was developed and implemented by a consortium of authors and interaction database groups.
A related interface called PSISCORE, provides programmatic access to interaction data scoring methods. This interface is currently discontinued until a new location is arranged for it.
"PSICQUIC" is pronounced like the English word "psychic" as in the ability to perceive information hidden from the normal senses through extrasensory perception.
A number of use cases are envisioned for these services. For example, once implemented by multiple interaction databases, they would allow a user to make a query for information at one database web-site and then have that query replicated at all other interaction databases (that have implemented the service interface). The user could then receive a compiled list of results that match their query regardless of the database that contains the information.
Note that only the first 15 columns of the iRefIndex MITAB files are returned from this service. The full data set is available via FTP download as described on the iRefIndex MITAB page and via iRefWeb.
WSDL locations:
Version information:
Available services:
All active services:
REST service samples:
- http://irefindex.vib.be/psicquic/webservices/current/search/query/species:4932
- http://irefindex.vib.be/psicquic/webservices/current/search/query/species:9606
More details about the project:
IntAct PSICQUIC View:
The format and content of the interaction data returned by these services is described on the README_MITAB2.6_for_iRefIndex page.
Changes from last version
There are major changes between iRefindex PSICQUIC service version 1.1.5 and version 1.1.6. In 1.1.5 the results returned were interaction-centric (one line in the results representing one binary interaction or a complex membership). From 1.1.6 onwards the results will be experiment-centric (one line per evidence per source). The new extended PSI MI-TAB (version 2.6) is used in the implementation, but only the first 15 columns will be available at the moment in order to maintain compatibility with other services. For further details on the returned results please refer the README_MITAB2.6_for_iRefIndex page.
The second major change is the usage of UniProt and RefSeq identifiers as uidA and uidB whenever that is possible.
Users are advised that there are differences between our implementation of these services and that of other databases. Most notably, interactions between 3 or more proteins (n-ary data) are represented in the PSI-MITAB files using a bi-partite model (one of the first two columns is used to represent the complex and the second column is used to represent a member of the complex). Other PSICQUIC services will likely use a spoke model representation.
Please refer to our documentation above and documentation provided by other PSICQUIC providers if you plan to combine results from multiple services.
Main iRefIndex Page
All iRefIndex Pages
Follow this link for a listing of all iRefIndex related pages (archived and current).
