| | 1 | = Overview = |
| | 2 | |
| | 3 | == Exchange format == |
| | 4 | |
| | 5 | It already exists an standard exchange format: PSI-MI. Two possibilities: |
| | 6 | |
| | 7 | * PSI-MI XML |
| | 8 | * PSI-MI TAB (tabulated) |
| | 9 | * [ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README Standard] |
| | 10 | * Expanded (!IntAct) - Additional columns to the standard, containing information like bait-prey, types, cross-references... |
| | 11 | |
| | 12 | == Service Providers == |
| | 13 | |
| | 14 | Service providers at the Hackathon |
| | 15 | |
| | 16 | * [http://www.ebi.ac.uk/intact IntAct] (Bruno Aranda, EBI) |
| | 17 | * DIP (Lukasz Salwinski, UCLA) |
| | 18 | * [http://string.embl.de STRING] (Michael Kuhn) |
| | 19 | * ... (please add yourself) |
| | 20 | |
| | 21 | == Service consumers == |
| | 22 | |
| | 23 | * Cytoscape (Keichiro Ono) |
| | 24 | * ... (please add yourself) |
| | 25 | |
| | 26 | = Existing Web Services = |
| | 27 | |
| | 28 | == !IntAct Web service == |
| | 29 | |
| | 30 | !IntAct already provides a very simple SOAP based web service (http://www.ebi.ac.uk/~intact/devsite/remote/binarysearch_ws.html) |
| | 31 | |
| | 32 | = Objectives = |
| | 33 | |
| | 34 | === Improve the existing !IntAct web service === |
| | 35 | |
| | 36 | Note: the !IntAct web service is in fact a web service that searches on a PSI-MI TAB file that contains all the interactions present at !IntAct. All the (java) code |
| | 37 | generated at !IntAct is open-source and licensed under the Apache Commons License 2.0. It means that this web service implementation could be used over any PSI-MI TAB file (not just the IntAct ones). |
| | 38 | |
| | 39 | * Taverna |
| | 40 | * !BioMoby |
| | 41 | * Check use-cases: |
| | 42 | * Get interaction or partners not only using Uniprot IDs (the primary identifiers for interactors used in !IntAct) |
| | 43 | |
| | 44 | === Define a common Interaction Query Language === |
| | 45 | |
| | 46 | It would be useful to have a common query language for interactions. Options: |
| | 47 | |
| | 48 | * [wiki:PSICQUIC] - we have agreed that the acronym is horrible :) |
| | 49 | * [http://lucene.apache.org] Lucene based searches over PSI-MI tab files - what is currently used in !IntAct. |
| | 50 | * This option seems to be the simplest according to the participants in the group, and could be a starting point. |
| | 51 | |
| | 52 | === Define specific use-cases === |
| | 53 | |
| | 54 | Cytoscape, as active consumer, has a bunch of use cases that can be a starting point to discuss how interaction data could be mined/queried. |
| | 55 | |
| | 56 | === Implementation of an Interaction DAS Server === |
| | 57 | |
| | 58 | Nothing specific has been said about this, but it was in the original agenda. |
| | 59 | |
| | 60 | = Important reminder = |
| | 61 | |
| | 62 | This is a wiki. Please, participate with your thoughts/additions/comments! :) |
