Cyndy Chandler 22 July 2011 Biological and Chemical Oceanography Data Management Office (BCO-DMO) SOST IWG-OP Biodiversity Ad Hoc Committee ~ July 2011 Quarterly Meeting ~ Washington, DC

bco-dmo.org Biological and Chemical Oceanography Data Management Office BCO-DMO What is BCO-DMO? Who is BCO-DMO? Why is BCO-DMO different? How do we accomplish our task? Outline Discussion: Data Management for Biodiversity Research

bco-dmo.org Biological and Chemical Oceanography Data Management Office BCO-DMO staff provide data management support for investigators and projects funded by NSF Ocean Sciences Biological and Chemical Oceanography Sections or NSF OPP ANT Organisms & Ecosystems Program partner with individual investigators and those associated with collaborative research projects data management support throughout the project capture and record documentation (metadata) sufficient to support data reuse and re-purposing load data and metadata into a relational database and ensure their availability online ensure final archive in appropriate data center (e.g. NODC); contribute to special repositories (e.g. CDIAC, OBIS, GenBank) ‘proposal to preservation’ What is BCO-DMO?

bco-dmo.org Biological and Chemical Oceanography Data Management Office BCO-DMO Staff Biology Department Peter Wiebe (Lead Investigator) Robert Groman (co-PI) Dicky Allison (Data Specialist) Tobias Work (Programmer) Marine Chemistry and Geochemistry David Glover (co-PI) Cyndy Chandler (co-PI) Stephen Gegg (Data Specialist) additional data specialists, consultants and collaborators as needed Who is BCO-DMO?

bco-dmo.org Biological and Chemical Oceanography Data Management Office BCO-DMO staff are funded to … support NSF OCE and OPP funded researchers ensure that data are … available to the research community in a timely manner sufficiently documented to facilitate reuse and re-purposing work with investigators during all phases of research: data management planning and stewardship proposal writing cruise preparation cruise and data documentation effective organization of data in the BCO-DMO data system permanent archive of data at NODC Why is BCO-DMO different?

bco-dmo.org Biological and Chemical Oceanography Data Management Office How do we accomplish our task? BCO-DMO staff work in partnership with PIs to create well-documented data sets from research programs involving a wide variety of sampling gear

bco-dmo.org Biological and Chemical Oceanography Data Management Office Data Discovery and Availability our primary task is to ensure that data from NSF OCE funded awards are freely available online the BCO-DMO data system and interfaces facilitate data discovery (text and map-based browse systems) data access to assess fitness-for-purpose data export and download data preservation in a permanent archive (the National Oceanographic Data Center (NODC)) How do we accomplish our task?

bco-dmo.org Biological and Chemical Oceanography Data Management Office Field Data to Database in situ data from research cruises are documented and contributed to the online data system and discoverable through a variety of user interfaces How do we accomplish our task? Original data from Bongo net tows and CTD/Niskin Rosette

bco-dmo.org Biological and Chemical Oceanography Data Management Office slide 9 of 17 MOCNESS data – paper to digital “Data Management in the Wild” ~ MOCNESS Data hauled in by people the samples are processed by people, observations recorded by people, and digital data sets created by people MOCNESS Sampling raw biology data raw physical data digital biology data digital physical data CTD sensor data

bco-dmo.org Biological and Chemical Oceanography Data Management Office slide 10 of 17 MapServer Starting Screen BCO-DMO Geospatial MapServer interface showing all available data.

bco-dmo.org Biological and Chemical Oceanography Data Management Office slide 11 of 17 MapServer with selections access to data

bco-dmo.org Biological and Chemical Oceanography Data Management Office BCO-DMO staff work in partnership with PIs to create well-documented data sets to enable reuse and re-purposing of data to support US contributions to large coordinated research programs and global ocean research themes How do we accomplish our task?

bco-dmo.org Biological and Chemical Oceanography Data Management Office BCO-DMO and Other Data Repositories BCO-DMO is part of a network of distributed data repositories working to support the research community and ensuring that data are available in the public domain. Carbon Dioxide Information Analysis Center North American Carbon Program Long Term Ecological Research Network National Center for Biotechnology Information: GenBank Rolling Deck to Repository (R2R) How do we accomplish our task?

bco-dmo.org Biological and Chemical Oceanography Data Management Office slide 14 of 17 “A scholar’s positive contribution is measured by the sum of the original data that he contributes. Hypotheses come and go but data remain.” In: Advice to a Young Investigator (Santiago Ramón y Cajal, 1897) Thank you. Questions? photo by Chris Linder (WHOI)

bco-dmo.org Biological and Chemical Oceanography Data Management Office What additional cyber-infrastructure is needed to support biodiversity research? What else is needed to support biodiversity research? The remaining slides are a supplement to the talk that may be useful during the data management discussion.

bco-dmo.org Biological and Chemical Oceanography Data Management Office NSF Dimensions of Biodiversity Program data from 9 awards to be managed by BCO-DMO NSF OCE # Dimensions: The Role of Viruses in Structuring Biodiversity in Methanotrophic Marine Ecosystems NSF OCE # and OCE # Dimensions: Significance of nitrification in shaping planktonic biodiversity in the ocean NSF OCE # , , and Dimensions: Biological controls on the ocean C:N:P ratios NSF OCE # and Dimensions: Uncovering the novel diversity of the copepod microbiome and its effect on habitat invasions by the copepod host What else is needed to support biodiversity research?

Marine Biodiversity Operation Network Extended research network being considered bco-dmo.org Biological and Chemical Oceanography Data Management Office slide 17 of 17

bco-dmo.org Biological and Chemical Oceanography Data Management Office Infrastructure Options Challenge: there are currently many sources with overlapping and/or incomplete information researchers must locate resources, resolve conflicts/duplicates, review and ‘repair’ retrieved data Strategies and Solutions: data warehousing - extract, transfer, load data data federation – network of distributed repositories data remain at the source and are retrieved on demand data aggregation – central catalog (e.g. EOL) What else is needed to support biodiversity research?

bco-dmo.org Biological and Chemical Oceanography Data Management Office Advantages and Disadvantages data warehousing – one central repository for all data one system ‘one stop shop’ is rarely appropriate for all data types data and information loss during transfer data federation – network of distributed repositories data remain closer to the ‘source of origin’ and local expertise data and information loss is limited requires negotiated arrangements (standards) to support interoperability of distributed systems Long-term preservation must be considered data aggregation (e.g. EOL) What else is needed to support biodiversity research?

bco-dmo.org Biological and Chemical Oceanography Data Management Office Interoperability the ability of different data repository systems to exchange and integrate data and information and present a unified view to the user requires syntactic (format) compatibility e.g. access/security, file formats, transfer protocols to retrieve data and information requires semantic (language) compatibility e.g. metadata standards, controlled vocabularies, ontologies to understand data and information What else is needed to support biodiversity research?

bco-dmo.org Biological and Chemical Oceanography Data Management Office Trans-disciplinary, cross-agency collaboration and cooperation a workshop of 100 invited participants held in Broomfield, Colorado in March 2011 NSF sponsored with support from USGS primary objective: “to substantially advance discussions and directions of data life cycle, data integration and data citation, with strong emphasis on end-use, and to provide a state-of-the-field report to NSF and the USGS of the geoinformatics community’s capabilities and needs... “ final report (in progress) Geo-Data Informatics 2011 Workshop Exploring the Life Cycle, Citation and Integration of Geo-Data What else is needed to support biodiversity research?

some thoughts... integration of distributed, loosely federated data repositories designed to foster biodiversity research and assessment Microbes to Mammals Habitat to Health Taxonomy to Tipping Points bco-dmo.org Biological and Chemical Oceanography Data Management What else is needed to support biodiversity research?

bco-dmo.org Biological and Chemical Oceanography Data Management Office Data repositories for biodiversity research? What else is needed to support biodiversity research? BCO-DMO LTER sites NCBI GenBank OBIS MICROBIS: ICoMM Marine Microbes Database EOL protein Data Bank (3D structures of DNA, RNA) Cell Image Library (cellimagelibrary.org) NOAA, NASA, EPA and USGS sites Literature (some are proprietary)

bco-dmo.org Biological and Chemical Oceanography Data Management Office Coordinating groups for biodiversity research? What else is needed to support biodiversity research? NSF, NOAA, NASA, EPA and USGS agency program managers, representatives, committees Interagency Working Groups and Advisory Committees Scientific Steering Committees Interagency Working Group on Ocean Observations (IWGOO) Support Office hosted at the Consortium for Ocean Leadership

Other considerations: What are the connection axes (geospatial, temporal, organism/taxon/species name)? PI name (e.g. Web of Science researcher ID; or ORCID - Open Source ID for researchers) Data provenance is very important Persistent identifiers (DOIs ?) References (reciprocal links) to published literature Access to proprietary information bco-dmo.org Biological and Chemical Oceanography Data Management What else is needed to support biodiversity research?

bco-dmo.org Biological and Chemical Oceanography Data Management Office Existing Repositories Other considerations: Long tail or ‘dark data’ (Heidorn 2008)

bco-dmo.org Biological and Chemical Oceanography Data Management Office Other considerations What are the use cases? Benedict, et al. 2007

bco-dmo.org Biological and Chemical Oceanography Data Management Office Final Slide What additional cyber-infrastructure is needed to support biodiversity research? What else is needed to support biodiversity research? Additional repositories? What about the *omics data? Connections between repositories? Standards (semantic and syntactic) Advisory groups, workshops and governance systems

bco-dmo.org Biological and Chemical Oceanography Data Management Office Existing Repositories

CDIAC Carbon Dioxide Information Analysis Center-Ocean CO2 TCO2 (DIC) TALK pH pCO2 CFCs SF6 CC14 CaCO3 DOC, TOC TDN dC14

OBIS - USA Ocean Biodiversity Information System (OBIS) - USA (will redirect)

GenBank SUBMIT DATA SEARCH for DATA