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-sourcesand add target/generated/java as a source folder - edit
docs/psicquic.properties.templateand put under/opt/stringdb/v10.0/psicquic.properties, but make sure it’s in sync withpsicquic-indexing-spring-test.xml - edit
docs/jdbc-v1.0.properties.templateand 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 |
|
| 8. First author | – |
| 9. publication id | – |
| 10&11. NCBI tax ids | species id(name) |
| 12. Interaction types |
|
| 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.