Resources for genomic observations from collection to analysis and publication

The space between standards and software, standards and other standards, and between software and other software, is what we are calling the "commons". The Biocode Commons is working with the standards community to ensure clear vocabularies and useful ontologies for biological resources and related assets through periodic workshops and hackathons. Links to the standards community are through the workings of the Genomic Biodiversity Working Group (partnering with GSC and TDWG). Biocode Commons is also collaborating on the development of the Biological Collections Ontology (BCO), working generally to better integrate ontologies, vocabularies, and relevant standards that are related to BCO.

Tools and Resources

Biosharing works to map the landscape of community developed standards in the life sciences, broadly covering biological, natural and biomedical sciences. ISA Tools helps you to provide a rich description of your experimental metadata. Biocode FIMS and LIMS are tools for tracking samples from the field field through the lab (FIMS/LIMS stands for Field/Laboratory Information Management System). The Biological Collections Ontology (GitHub site) is an effort to model genomic biodiversity and related samples and processes, building off of the BFO, OBI, MIxS, and Darwin Core.

Biocode Commons Workshops and Hackathons

Periodic workshops and hackathons, sponsored by Biocode Commons, in conjunction withthe RCN4GSC, I3BEager, and BiSciCol NSF grants. Community Next Steps for Making Globally Unique Identifiers Work for Biocollections Data (October, 2014) In order to further progress towards a broader community consensus on globally unique identifiers, a group of biocollections and informatics experts assembled in Stockholm in October 2014 to discuss community next steps to overcome current roadblocks for implementing globally unique identifiers for biocollections. See the article in Zookeys Identifying Practical Applications of Ontologies, Eugene, Oregon (August, 2014). Meeting report in press. The workshop looked at terms in Darwin Core and Audubon Core into a Biological Collections Ontology (BCO) framework. In addition, the workshop participants reviewed technical specifications and approaches for annotating instance data with BCO terms. Also, laid out proposed activities for the next 3 to 18 months to continue this work Genomic Biodiversity Working Group / Biocode Commons Hackathon at the GSC16 meeting, Oxord, UK (April 1-2, 2014). This hackathon was focused on building components of the Biological Collections Ontology and creating a MaterialSample Core using GBIF's Integrated Publishing Toolkit Biological Collections Ontology / Population and Community Ontology Coding Workshop at the University of Arizona (February, 2014). See the published Meeting Report. Biological Collections Ontology / Biocode Commons Hackathon, GSC14 (September, 2012) Berkeley, BiSciCol, BigData, Identifiers, and VertNet (3Biv) (August, 2012) Biocode Moorea Genomic Observatory Workshop (June, 2012) Semantics of Biodiversity Workshop at KU (May, 2012)