| 9 | | == Goals == |
| 10 | | |
| 11 | | * What is the best solution for integration of the web services? |
| 12 | | * Is the list of BioMOBY objects is clean enough to treat with the client program? How about the inheritance? |
| 13 | | * Why BioMOBY doesn't use SOAP's complexType instead of the BioMOBY triple (original XML) data structure? |
| 14 | | * Is there any performance bottleneck in the current system of the BioMOBY? |
| 15 | | * How to integrate arising new data structures such as pathways, metabolomics, and proteomics? |
| 16 | | * What can be done with the Open Bio* projects to support interoperability? |
| 17 | | * How to integrate non-MOBY web service providers (Japanese DDBJ, KEGG, PDBj, CBRC services + EBI, NCBI services) |
| 18 | | |
| 28 | | But the set of data types and methods gathered in BioMOBY looks redundant and complicated to generate typical workflows for end users. |
| 29 | | Besides, some of the major service providers are not included in the BioMOBY framework yet. |
| 30 | | In DBCLS, we are trying to develop a new proxy server which translates user's request for the appropriate web service provider. |
| 31 | | The server will also converts the query and result to the simplified/unified data types, say "50 basic bioinformatics data types" (might be a subset of BioMOBY). |
| 32 | | Anyway, interoperability can be significantly improved if all Bio* libraries supports them and we just need a practical environment for bioinformatics. |
| 33 | | Thus, we believe gathering all web service providers and Open Bio* library developers to disucuss about the standardization of objects and methods among web services and programming languages must benefit usability and interoperability for the life science in the next era. |
| | 19 | However, there are many major service providers are not yet participated in the BioMOBY framework. |
| | 20 | Especially, there are several web service providers in Japan such as DDBJ, KEGG, PDBj and CBRC but none of them are not integrated in any context. |
| 35 | | * Utilizing every bioinformatics web services by 4 major computer languages |
| 36 | | * Standardizing the objects and methods in bioinformatics web services |
| 37 | | * Creating compatible classes for sequences, expressions, pathways etc. among Open Bio* libraries |
| | 22 | Thus, at [http://www.dbcls.jp/en/ DBCLS], we started to develop a new proxy server which translates user's request for the appropriate web service provider. |
| | 23 | If all [http://www.open-bio.org/ Open Bio*] libraries support BioMOBY and other service providers, interoperability of these services can be significantly improved. |
| | 24 | Here, we need agreement for the future web services with every web service providers and client developers. |
| | 25 | |
| | 26 | We believe gathering all web service providers to disucuss about the standardization of objects and methods among web services, |
| | 27 | and Open Bio* library developers from different programming languages to discuss about the implementation of the common infrastructure, |
| | 28 | must benefit usability and interoperability for the life science in the next era. |
| | 29 | |
| | 30 | For this purpose, we hope to organize a BioHackathon specialized for the web services in 2008. |
| | 31 | |
| | 32 | * Standardizing the objects and methods in bioinformatics web services (BioMOBY) |
| | 33 | * Discuss about the best solution of the framework and ontologies for the future in life science |
| | 34 | * Utilizing every bioinformatics web services by 4 major computer languages (Perl, Python, Ruby, Java) |
| | 35 | * Creating compatible classes for sequences, expressions, pathways etc. among Open Bio* libraries |
| 49 | | |
| 50 | | === BioMOBY === |
| 51 | | |
| 52 | | I would like to ask Dr. Mark Wilkinson to give us a lecture for the following objectives: |
| 53 | | |
| 54 | | * to make every web service providers understand what does the BioMOBY is |
| 55 | | * current status of the BioMOBY project and how the sites integrated by BioMOBY works |
| 56 | | * current status of the semantic MOBY and its practical usages or goals |
| 57 | | |
| 58 | | and I would like to discuss about: |
| 59 | | |
| 60 | | * what kind of efforts have been made to popularize BioMOBY |
| 61 | | * why all web services are not compatible with BioMOBY yet? |
| 62 | | * what is the strength of BioMOBY compared with non-BioMOBY web services? |
| 63 | | * what kind of improvements can be made from now? |
| 64 | | * which languages can be used to create BioMOBY clients (only Perl and Java for now?) |
| 65 | | * refine the ontology for data types and methods |
| 66 | | * implement BioMOBY client library in every Bio* projects |
| 67 | | * utilize BioMOBY in NCBI, EBI, KEGG, DDBJ etc. or to create a proxy server which converts these services compatible with BioMOBY |
| 68 | | |
| 69 | | === Open Bio* === |
| 70 | | |
| 71 | | to be written... |
| 72 | | |
| 73 | | === Clients (Taverna, G-language etc.) === |
| 74 | | |
| 75 | | to be written... |
| 76 | | |
| 77 | | === Web Service providers === |
| 78 | | |
| 79 | | to be written... |
| 80 | | |
| 81 | | * How to increase the number of SOAP compliant services (tools/databases) |
