IntAct NAR 2010

Organisation of the NAR 2010 IntAct paper

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IntAct NAR 2010 by Mind Map: IntAct NAR 2010

1. Future Development

1.1. new MITAB format

1.2. more features to the web site

1.2.1. MyIntAct

1.2.1.1. notify me when new data is released

1.2.2. Molecule set search

1.2.3. Other ?

1.3. new curation tool

1.4. IMEx exchange

2. Abstract (200 words max)

3. Intro

3.1. data growth and need to cope with it

3.2. why did we need a new web site

3.2.1. Limitation of the old web site

3.2.1.1. performance

3.2.2. better UI for users

3.2.3. addressing emerging user needs

3.3. from ppi interaction database to molecular interaction database

4. Discussion

4.1. intact community

4.1.1. intact-users

4.1.2. intact-developers

4.2. aims to do weekly releases

5. New web site

5.1. find a dataset to use as example

5.2. rational

5.2.1. binary interaction representation

5.2.2. evidence based browsing

5.2.3. tab oriented web site

5.3. searching

5.3.1. MIQL

5.3.1.1. refer to PSICQUIC paper

5.3.2. ontology support

5.3.2.1. which ontologies

5.3.2.2. suggestions

5.3.3. compound substructure search

5.3.4. advanced field search (uniprot like)

5.4. interaction table

5.4.1. configure the view

5.4.2. filter spoke expanded interactions

5.4.3. more export formats

5.4.3.1. refer to XML and TAB APIs

5.4.4. sorting

5.4.5. opening the detailed view

5.5. interaction details

5.5.1. overall description

5.5.2. how to find similar interactions

5.6. browsing

5.6.1. By ontology

5.6.1.1. GO

5.6.1.2. Chebi

5.6.2. By molecule type

5.6.3. Linkout

5.6.4. By Uniprot Taxonomy

5.7. List view

5.7.1. molecule involved by type

5.7.2. linkout

5.8. molecule view (Dasty2)

5.9. visualization

5.9.1. Simple view (HV)

5.9.2. cytoscape integration

6. Curation

6.1. standards

6.2. dataset

6.3. complexes

6.4. data stats

6.4.1. breakdown protein/SM if MSD/DrugBank imported

6.5. CVs

6.6. data submission

6.6.1. how to get in touch ?

6.6.2. privacy statement

7. Other ideas

7.1. PSI-MI XML 1.0 to be retired

7.2. tabular data

7.3. Data model supports confidence

8. Local Installation

8.1. point to the local install page

8.1.1. page does not exist though

8.2. local install

8.2.1. can support small scale

8.2.2. can support large production grade

8.2.3. technical requirements

8.2.3.1. RDBMS

8.2.3.2. web server

8.2.3.2.1. web site

8.2.3.2.2. solr

9. TODOs

9.1. check if dataset are in the advanced search

9.2. add dataset description page

9.2.1. list of clickable dataset

9.3. add curated complex page

9.4. Add documentation on how to setup Solr

9.5. Add code sample illustrating how to use intact-core 2.0.x

9.6. import DrugBank

9.7. import MSD data

9.8. release artifacts at Google Code

9.8.1. TAB

9.8.2. XML

9.8.3. intact-kickstart

9.8.3.1. source with deps

9.8.3.2. source without deps

9.9. Did you know ?

9.9.1. programatic access to intact

9.10. intaction tab: add link to programatic access

9.11. Fix gene name queries in intact-view

9.12. Fix ontology suggestion selection

10. Libraries and APIs

10.1. point out to code snippets (kickstart)

10.2. library availability

10.2.1. open source

10.2.2. where to find them

10.2.2.1. link to Google Code

10.3. Rintact & Rpsimixml

10.4. Remote API

10.4.1. PSICQUIC