MEDFORD- RNASeq: A human and machine readable markup language to facilitate FAIR coral metadata
Creators: name: Freeman, John
name: Ashey, Jill
name: Shpilker, Polina
name: McKelvie, Hailey
name: Putnam, Hollie
name: Greenberg, Jane
name: Cowen, Lenore J
name: Couch, Alva
name: Daniels, Noah
Publisher: name: F1000 Research Limited
Year: 2020

description: <b>Corals are home to vast biodiversity and play a critical role protecting shores from degradation. Research into RNA expression can be used to examine coral responses to stressors. The corals research community has long been committed to sharing and open data formats, and both individual researchers and large funding agencies have invested heavily in making data available [1-3], but the standard formats in which these metadata are recommended to be structured so that they are FAIR (Findable, Accessible, Interoperable, and Reusable) [4] such as RDF [5] or CoRIS [6], are not designed to be easily readable or writable by humans as opposed to machine creators. This is particularly a barrier when the humans generating the metadata are not programmers.</b><br> <b>We introduce a preliminary design for MEDFORD, a markup language file format that is designed to be simultaneously human and machine writable and readable. We take inspiration from the highly successful flat file format of the Protein Data Bank (PDB) [7] that stores complex files with protein sequence, 3D spatial structural data, author and reference data, plus comments and so on, in a format designed to be human readable, machine readable, and extendable to allow additional types of fields without breaking the ability to parse older PDB files. </b><br> <b> </b><br> <b> Our first use case is for coral holobiont transcriptomics data (e.g., RNASeq, one of the most powerful and common types of omics experiments to explore the genetic basis of factors that lead to coral resilience or vulnerability to environmental stressors), where we build the needed complexity to manage spatial-temporal holobiont expression metadata into MEDFORD from the start.. A coral researcher, untrained in programming and not a database expert, will be able to directly produce and interpret MEDFORD files, and we are currently writing the back-end parser that will be able to automatically translate MEDFORD files into existing file format standards for depositing in databases and repositories [8]. MEDFORD will enable transcriptomic data to be findable, accessible, and interoperable, where we are currently building the back-end infrastructure to translate between MEDFORD and make it compatible with other existing databases and systems such as RDF, ultimately supporting the reusability “R” in FAIR as well.</b><br> <br> <br> <b>[1] Liew, Y.J., Aranda, M. and Voolstra, C.R., 2016. Reefgenomics.Org - a repository for marine genomics data. Database, 2016. baw152.</b><br> <b> </b><br> <b>[2] Madin, J.S., Anderson, K.D., Andreasen, M.H., Bridge, T.C., Cairns, S.D., Connolly, S.R., Darling, E.S., Diaz, M., Falster, D.S., Franklin, E.C. and Gates, R.D., 2016. The Coral Trait Database, a curated database of trait information for coral species from the global oceans. Scientific Data, 3(1), pp.1-22.</b><br> <b> </b><br> <b>[3] Zaslavsky, I., Valentine, D., Richard, S.M., Gupta, A., Meier, O., Peucker-Ehrenbrink, B., Hudman, G., Stocks, K.I., Hsu, L., Whitenack, T. and Grethe, J.S., 2017. EarthCube Data Discovery Hub: Enhancing, Curating and Finding Data across Multiple Geoscience Data Sources. AGUFM, 2017, pp.IN21B-0049.</b><br> <b> </b><br> <b>[4] Wilkinson, M.D., Dumontier, M., Aalbersberg, I.J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.W., da Silva Santos, L.B., Bourne, P.E. and Bouwman, J., 2016. The FAIR Guiding Principles for scientific data management and stewardship. Scientific data, 3(1), pp.1-9.</b><br> <b> </b><br> <b>[5] Grobe, M., 2009, October. Rdf, jena, sparql and the 'semantic web'. In Proceedings of the 37th annual ACM SIGUCCS fall conference: communication and collaboration (pp. 131-138).</b><br> <b> </b><br> <b>[6] O'Connor, S, Mason, Z, Zhou, Y. and R. Wenker, (2020). NOAA Coral Reef Information System, National Centers for Environmental Information. Silver Spring, MD, 2p.</b><br> <b> </b><br> <b>[7]Young, J.Y., Westbrook, J.D., Feng, Z., Peisach, E., Persikova, I., Sala, R., Sen, S., Berrisford, J.M., Swaminathan, G.J., Oldfield, T.J. and Gutmanas, A., 2018. Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. Database, 2018.</b><br> <b> </b><br> <b>[8] Groman, R.C., Allison, M.D., Chandler, C.L., Copley, N.J., Gegg, S.R., Glover, D.M., Kinkade, D.B., Rauch, S.M., Shepherd, A. and Wiebe, P.H., 2014. Progress in Data Discovery and Access: The Next Steps.</b>