{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T19:16:45Z","timestamp":1784920605890,"version":"3.55.0"},"reference-count":20,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2022,8,17]],"date-time":"2022-08-17T00:00:00Z","timestamp":1660694400000},"content-version":"vor","delay-in-days":228,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"NSF-OAC","award":["1939263"],"award-info":[{"award-number":["1939263"]}]},{"name":"NSF-OAC","award":["1939795"],"award-info":[{"award-number":["1939795"]}]},{"name":"HDR-BIO NSF-OAC","award":["1940233"],"award-info":[{"award-number":["1940233"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,8,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Reproducibility of research is essential for science. However, in the way modern computational biology research is done, it is easy to lose track of small, but extremely critical, details. Key details, such as the specific version of a software used or iteration of a genome can easily be lost in the shuffle or perhaps not noted at all. Much work is being done on the database and storage side of things, ensuring that there exists a space-to-store experiment-specific details, but current mechanisms for recording details are cumbersome for scientists to use. We propose a new metadata description language, named MEtaData Format for Open Reef Data (MEDFORD), in which scientists can record all details relevant to their research. Being human-readable, easily editable and templatable, MEDFORD serves as a collection point for all notes that a researcher could find relevant to their research, be it for internal use or for future replication. MEDFORD has been applied to coral research, documenting research from RNA-seq analyses to photo collections.<\/jats:p>","DOI":"10.1093\/database\/baac065","type":"journal-article","created":{"date-parts":[[2022,8,17]],"date-time":"2022-08-17T14:47:38Z","timestamp":1660747658000},"source":"Crossref","is-referenced-by-count":7,"title":["MEDFORD: A human- and machine-readable metadata markup language"],"prefix":"10.1093","volume":"2022","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6761-7326","authenticated-orcid":false,"given":"Polina","family":"Shpilker","sequence":"first","affiliation":[{"name":"Department of Computer Science, Tufts University , 177 College Ave, 02155, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Freeman","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Tufts University , 177 College Ave, 02155, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hailey","family":"McKelvie","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Tufts University , 177 College Ave, 02155, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jill","family":"Ashey","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Rhode Island , 120 Flagg Rd, 02881, RI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jay-Miguel","family":"Fonticella","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Tufts University , 177 College Ave, 02155, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hollie","family":"Putnam","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Rhode Island , 120 Flagg Rd, 02881, RI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane","family":"Greenberg","sequence":"additional","affiliation":[{"name":"Metadata Research Center, College of Computing & Informatics, Drexel University , 3675 Market Street, 19104, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6698-6413","authenticated-orcid":false,"given":"Lenore","family":"Cowen","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Tufts University , 177 College Ave, 02155, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alva","family":"Couch","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Tufts University , 177 College Ave, 02155, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9538-825X","authenticated-orcid":false,"given":"Noah M","family":"Daniels","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Statistics, University of Rhode Island , 9 Greenhouse Rd, 02881, RI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,8,17]]},"reference":[{"key":"2022081714473231600_R1","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/j.zool.2011.04.001","article-title":"Metaorganisms as the new frontier","volume":"114","author":"Bosch","year":"2011","journal-title":"Zoology"},{"key":"2022081714473231600_R2","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1038\/nature22901","article-title":"Coral reefs in the anthropocene","volume":"546","author":"Hughes","year":"2017","journal-title":"Nature"},{"key":"2022081714473231600_R3","doi-asserted-by":"publisher","first-page":"1023","DOI":"10.1111\/1365-2435.13331","article-title":"Coral reef ecosystem services in the Anthropocene","volume":"33","author":"Woodhead","year":"2019","journal-title":"Funct. 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