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The official string-db.org PSICQUIC implementation.

Important note

The STRING-DB PSICQUIC API is not equivalent/compatible with the STRING-DB’s API :

  • it provides just a subset of all data available (only the core species – 417 out of 1133 in v9.1), and only interactions with score > 400 are indexed)
  • each STRING-DB evidence channel is reported as a separate interaction (homology excluded, all transferred combined into one)

How to setup development environment

  • get JDK 1.7 (or newer) and Maven 3
  • run mvn generate-sources and add target/generated/java as a source folder
  • edit docs/psicquic.properties.template and put under /opt/stringdb/v10.0/psicquic.properties, but make sure it’s in sync with psicquic-indexing-spring-test.xml
  • edit docs/jdbc-v1.0.properties.template and save at /opt/stringdb/jdbc-v1.0.properties

How to export MiTab files

As of v10 we will not be running the REST service but only provide mitab files for download. To generate them run:

MAVEN_OPTS=" -Xmx16g " mvn -PexportMitab install

To index (will take days to finish..)

Run: MAVEN_OPTS=" -Xmx2559m " mvn -PcreateIndexWithSolrRunning install

To try locally

Run: mvn -DskipTests=true -Pstart-jetty-solr package jetty:run

This will start jetty locally which can be accessed at
http://localhost:9090/psicquic/webservices/current/search/query/species:9606?firstResult=0&maxResults=10

Mapping string-db data to PsiMitab

This section explains how is string-db’s database data converted to PsiMiTab format for indexing.
The reference is MITAB27Format .

MiTab Column Header
1&2. unique identifier external_id and uniprotId
3&4. alternative identifiers uniprot & refseq
5&6. aliases preferred protein name
7. Interaction detection methods

  • textmining “MI:0087”(predictive text mining)

  • co-occurrence “MI:0085”(phylogenetic profile)

  • co-expressions “MI:0686”(unspecified method – coexpression)

  • fusion “MI:0036”(domain fusion)

  • neighbourhood “MI:0057”(gene neighbourhood)

  • database "MI:0362”(inferrence)

  • experimental “MI:0045”(experimental interaction detection)

  • transfers “MI:0064”(interologs mapping)

8. First author
9. publication id
10&11. NCBI tax ids species id(name)
12. Interaction types

  • experimental “MI:0914”(association)

  • database “MI:1110”(predicted interaction)

  • all other “MI:1110”(predicted interaction)
13. source db for experimental & database channels, map {protein_id → collection_id} using evidence.sets_items and from evidence.sets, then map
{collection_id → miterm} as following:

for all other channels: psi-mi:“MI:1014”(string)
14. interaction ID we don’t have them
15. score For non-transferred channels (except homology) its as reported in the database.
All transferred channels (except homology) – are combined into one score.
See StringDbScores#getTransferredScore for details.
16. Complex expansion
17 & 18. Biological roles ID: MI:0499 (unspecified role), go to the source DB to find out
19&20. Experimental roles ID: MI:0499 (unspecified role), go to the source DB to find out
21&22. Interactor types ID: MI:0326 Name: protein
23&24. Xref for interactors
25. Xref for the interaction
26&27. Annotations for interactors
28&29 Annotations for the interaction
30. Host id
31. Creation date
32. Update date
33 & 34 Interactors checksums ROGID
35. Interaction checksum
36. Negative interaction
37 & 38. Features
39 & 40. Stoichiometry
41 & 42. Participant identification method

References

Solr cheat sheet

curl 'http://localhost/psicquic/update?pp=true' -H "Content-Type: text/xml" --data-binary '<rollback/>'
curl 'http://localhost/psicquic/update?pp=true' -H "Content-Type: text/xml" --data-binary '<delete><query>*:*</query></delete>'

Contact

For any questions, comments, remarks, drop me an email

License

This software is licensed under the Apache 2 license, quoted below.

Copyright 2017 University of Zürich, SIB, and others.

Licensed under the Apache License, Version 2.0 (the "License"); you may not
use this file except in compliance with the License. You may obtain a copy of
the License at

    http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
License for the specific language governing permissions and limitations under
the License.