| | 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 | |
