AuthorReagentTable:aproposalMadelineCrosby,NorbertPerrimon,andtheFlyBaseConsortium*
DepartmentofMolecularandCellularBiology,HarvardUniversity
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Inconsultationwithothermodelorganismdatabases,FlyBase hasformulatedaprototype"authorreagenttable"(ART).Ourgoalistofacilitatehandlingofreagentsourceandidentifierinformationatmultiplesteps,benefitingresearchers,journals,andbiologicaldatabases.TheproposedARTisintheformatofaspreadsheetwithstandardizedcolumnsandinvariantrowlabels.Itisdesignedtobeusedregularlyduringthecourseofaresearchproject,recordingreagentsastheyarereceivedand/orused.Lab-wideuseofsuchacommonreagentformwouldfacilitatetrackingofreagentswithinthelab.Atthepointofsubmissionofamanuscript,withacompletedARTinhand,provisionofreagentdatawouldbeverystraightforward,particularlytojournalsusingformattedsubmissionsystemssuchasSTARMethods(Marcus,E.etal.,2016;PMID:27565332).Useofreagentidentifiersisoneofthekeyrequirementsofthesystem,encouragingtheuseofdatabaseandstockcenteridentifiers,RRIDs(Bandrowski,A.etal.,2016;PMID:26589523),andcatalognumbersforcommercialproviders.Wideruseofidentifiersandrecognizedsymbolswouldincreasethetransparencyandreproducibilityofbiologicalresearch,whilefacilitatingcuration intoresearchdatabases.Forgeneticexperiments,unambiguousidentificationofthegenesstudiedcouldbeanadditionalcomponentoftheART.AsecondarygoalofthisproposedsystemistoencouragejournalstomakesuchdataavailableasdownloadableTSVs,spreadsheetsorsimilarformats.Theauthorreagenttablecouldalsobeincorporatedintotheevolvinguseofpreprintrepositories:anARTcouldsimplybeappendedtothepreprintmanuscript.Feedbackonthisproposalfromthelargerbiocuration communitywouldbemostwelcome.Addendum:Geneticshasnowadoptedtheauthorreagenttable;seetheir“PreparingManuscriptsforSubmission”page.
Thetemplateandexamplecanbedownloadedfromflybase.org/journal/reagent_form.
• Intheformofaspreadsheetthatcanbeusedregularlyduringthecourseofaresearchproject,recordingreagentsastheyareused.
• Wouldfacilitatetrackingwithinalab.
• Ifthesameformatisusedformanuscriptsubmissions,requiresonlyminoreditingonthepartoftheresearcher.
• JournalswouldreceivereagentinformationinaformatthatisstraightforwardtohandleandthatallowsdownloadsasTSVformatorspreadsheet.
• Wideruseofidentifiersandparsable formatswouldbeahugehelpforbiologicaldatabases.
• Awidelyusedstandardizedformatwouldfacilitatepropagationofaccuratereagentinformation,allowingimportofexistingentriesintoanewtable.
Rowsduplicatedasneeded(onerowforeachreagent).
Rowtitlesmustremainunchanged;ordercanbechanged;unusedcategoriescanberemoved.
Designedtofacilitateautomatedparsing:
Colorsentirelyoptionalandcanbechanged.
Columnorderandtitlesmustremainunchanged.
Standardizedtemplateprovidedtoresearchers.
GeneticsandG3areencouraginguseoftheReagentTable.
Theyarealsosolicitingfeedbackfromauthors.
Additionaljournalsarebeingcontacted.
OpportunitytoencourageuseofRRIDs.(https://scicrunch.org/resources)
Wewelcomefeedbackonthisproposal,fromresearcherswithinandoutsidethemodelorganismcommunities,frombiocurators,andfromanyotherinterestedparties.
Allfeedbackishelpful– whetherdetailedandspecific,ormoregeneral.Weareespeciallyinterestedinadditionaldatatypesthatshouldbeadded.
Pleasecontact:Madeline(Lynn)[email protected]
Multipleoutstandingissues,forexample:
ShouldtherebeadedicatedcolumnforRRIDs?(Wouldthatdiscourageuseofotheridentifiers?)
Ideally,theuseofstandardidentifierswouldfacilitaterigoroussearchesoftheliterature.Thisproposaldoesnotaddressthatissue,sinceareagenttableaspartofsupplementaryinformationwouldnotbevisibletomosttext-mining.
*Members of the FlyBase Consortium (flybase.org): Norbert Perrimon, Susan Russo Gelbart, Julie Agapite, Kris Broll, Madeline A. Crosby, Gilberto do Santos, David B. Emmert, L. Sian Gramates, Kathleen Falls, Beverley B. Matthews, Christopher J. Tabone, Pinglei Zhou, Mark Zytkovicz (FlyBase-Harvard), Nicholas H. Brown, Giulia Antonazzo, Helen Attrill, Silvie Fexova, Phani Garapati, Tamsin Jones, Aoife Larkin, Steven J. Marygold, Gillian H. Millburn, Alix J. Rey, Vitor Trovisco, Jose-Maria Urbano (FlyBase-Cambridge), Thomas Kaufman, Bryon Czoch, Joshua L. Goodman, Gary B. Grumbling, Victor B. Strelets, Jim Thurmond (FlyBase-Indiana), Richard Cripps, Maggie Werner-Washburne, Phillip Baker (FlyBase-New Mexico).
FlyBase is supported by a grant from the National Human Genome Research Institute (NHGRI) at NIH #U41HG000739; support is also provided by the British Medical Research Council.
ABSTRACT
ManythankstomembersofZFIN,SGD,WormBase,MGI,andtheFlyBase SABforinputandthoughtfulfeedback.
