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gmicklem edited this page Jul 30, 2013
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Welcome to the [BioHackathon 2013] (http://2013.biohackathon.org/) Wiki!
- BioHackathon 2013 symposium slides
- Instructions to Authors (all BioHackers are authors!) AuthorInstructions
Topics may cover the following domains, but are not limited to:
- [RDFization (SDKs, Bio*, toolkits, naming conventions & dataset registries, minimum descriptions, annotation and linking strategies)] (https://github.com/dbcls/bh13/wiki/RDFization)
- [RDFization (minimum descriptions for the dataset)] (https://github.com/dbcls/bh13/wiki/RDFization_dataset)
- [RDF hosting (e.g. triple store deployment and performance, SPARQL endpoint control and monitoring, availability, content summarization, and syndication)] (https://github.com/dbcls/bh13/wiki/RDFhosting)
- [ontology-based data integration for specific domains (e.g. genomics, proteomics, glycomics, pathways & interactions, gen2phen; using SIO/BFO2, etc)] (https://github.com/dbcls/bh13/wiki/Ontology-based-data-integration)
- (Semantic) web services & interoperability (SADI, candidate services, SPARQL endpoints to services)
- (Semantic) web applications (CORS & ajax/jquery service invocation, facet browsing, visualization)
- [Text-mining, NLP and ontology mapping (LODQA, BioPortal, NanoPublication, Annotation Ontology, etc.)] (https://github.com/dbcls/bh13/wiki/Text-mining,-natural-language-processing,-and-ontology-mapping)
- [RDF/Ontology on Human transcript database] (https://github.com/dbcls/bh13/wiki/humgenes) H-InvDB (http://h-invitational.jp/hinv/ahg-db/index.jsp) including Gene, Protein, genome
- [RDF/Ontology on Glycoscience data] (https://github.com/dbcls/bh13/wiki/Glycogroup)
- OpenBio miscellaneous coding (BioRuby, ...)
- RDF/Ontology on Drug discovery data
- CurateIt! - a lightweight, web-based annotation tool
- Biological Data Visualization
- MBGD
- Wikidata and SemanticMediaWiki
- YummyData
- RDF/ontology on PPI/PLI data
- MicrobeDB.jp
- G-language Project
- VoID descriptions for InterMine and UniProt, sparql for InterMine
- Use available SDKs/toolkits to generate RDF.
- Use [Identifiers.org] (http://identifiers.org/) URIs to interconnect resources.
- Provide [Dataset descriptions] (https://docs.google.com/spreadsheet/ccc?key=0Aoy0zfdRviKsdFJWTDFpblNXc3BtelhrdEpNYTdvbXc) for your RDF data. (for RDF data of DB catalog : [BioDBCore] (http://www.biosharing.org/), [Integbio DB Catalog] (http://integbio.jp/dbcatalog/?lang=en), Indetifiers.org
- Use [Bio2RDF] (http://bio2rdf.org/) and EdgeStore database (under construction) for resolving link information and data retrieval with/from original databases.
- Create RDF/OWL version of the [Identifiers.org] (http://identifiers.org/) repository by introducing [VoID] (http://www.w3.org/TR/void/) vocabulary and defining database classes.
- Following [UniProt] (http://beta.sparql.uniprot.org/) and [PDB] (http://rdf.wwpdb.org/pdb/) databases, convert major reference datasets such as BioProject/RefSeq and [GFF/GVF] (http://www.biointerchange.org/ontologies.html) into RDF with common ontologies such as [FALDO] (https://github.com/JervenBolleman/FALDO), [SIO] (http://code.google.com/p/semanticscience/wiki/SIO) and many others found in [BioPortal] (http://bioportal.bioontology.org/) / [OBO] (http://www.obofoundry.org/).
- Generate and collect distributed annotations from the community as [nanopublications] (http://nanopub.org/).
- Statistical metrics and quality assessments ([VoID] (http://www.w3.org/TR/void/), [Bio2RDF] (https://github.com/bio2rdf/bio2rdf-scripts/wiki/Bio2RDF-dataset-metrics), [YummyData] (http://yummydata.org/), OpenPHACTS)
- Enable [CORS] (http://www.w3.org/TR/cors/) by adding an "Access-Control-Allow-Origin *" header.
- How to monitor and protect your endpoint? (SPARUL, killer queries)
- Index downloadable data with sindice
- Embed [Schema.org] (http://www.w3.org/wiki/WebSchemas/BioDatabases) metadata on web pages.
- Register endpoint with thedatahub, identifiers.org?
- Use [OpenSearch] (http://www.opensearch.org/) standards for describing search & results.
- YummyData bio-sparql endpoints monitoring service
- Use [SADI] (http://sadiframework.org/) framework for automated discovery.
- Map input/output descriptions to [SIO] (http://sio.semanticscience.org).
Wednesday morning excursion options here: http://tinyurl.com/bh13exc
The meeting hashtag was #biohack13,
- BioHackathon 2013 Sunday Symposium & SkyTree
- BioHackathon 2013 Monday & Tuesday
- [BioHackathon 2013 Wednesday to Friday] (http://storify.com/pjacock/biohackathon-2013-wednesday-onwards)
- BioHackathon 2013 Friday Wrap-up