| 1 | = Tools = |
| 2 | |
| 3 | Creating generic-yet-usable end user tools that work directly with the RDF graph data model. |
| 4 | |
| 5 | == Open Bio* == |
| 6 | |
| 7 | * Common API |
| 8 | * User-side APIs |
| 9 | * DB-side APIs (for triple store, Linked Data on the web) |
| 10 | |
| 11 | * Programs |
| 12 | * Data format converters |
| 13 | * Tools for import/export/search |
| 14 | |
| 15 | * Projects |
| 16 | * BioRuby |
| 17 | * BioPython |
| 18 | * BioPerl |
| 19 | * BioJava |
| 20 | * BioLib |
| 21 | |
| 22 | == Text mining == |
| 23 | |
| 24 | * GO PubMed |
| 25 | * NER for genes, diseases, drugs |
| 26 | * MEDIE |
| 27 | * Query builder from natural language |
| 28 | |
| 29 | == Storage == |
| 30 | |
| 31 | * Existing triple stores |
| 32 | * Virtuoso |
| 33 | * ORACLE |
| 34 | * : |
| 35 | |
| 36 | * Evaluation |
| 37 | * Scale? |
| 38 | * Speed |
| 39 | * Interface |
| 40 | |
| 41 | == End-user software == |
| 42 | |
| 43 | * Cytoscape |
| 44 | * BioMart |
| 45 | * InterMine |
| 46 | * Galaxy |
| 47 | * G-language |
| 48 | |