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  • Author Reagent Table: a proposal 70 - FlyBase · 2017. 4. 5. · Author Reagent Table: a proposal Madeline Crosby, Norbert Perrimon, and the FlyBase Consortium* Department of Molecular
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Author Reagent Table: a proposal Madeline Crosby, Norbert Perrimon, and the FlyBase Consortium* Department of Molecular and Cellular Biology, Harvard University 70 In consultation with other model organism databases, FlyBase has formulated a prototype "author reagent table" (ART). Our goal is to facilitate handling of reagent source and identifier information at multiple steps, benefiting researchers, journals, and biological databases. The proposed ART is in the format of a spreadsheet with standardized columns and invariant row labels. It is designed to be used regularly during the course of a research project, recording reagents as they are received and/or used. Lab-wide use of such a common reagent form would facilitate tracking of reagents within the lab. At the point of submission of a manuscript, with a completed ART in hand, provision of reagent data would be very straightforward, particularly to journals using formatted submission systems such as STAR Methods (Marcus, E. et al., 2016; PMID:27565332). Use of reagent identifiers is one of the key requirements of the system, encouraging the use of database and stock center identifiers, RRIDs (Bandrowski, A. et al., 2016; PMID:26589523), and catalog numbers for commercial providers. Wider use of identifiers and recognized symbols would increase the transparency and reproducibility of biological research, while facilitating curation into research databases. For genetic experiments, unambiguous identification of the genes studied could be an additional component of the ART. A secondary goal of this proposed system is to encourage journals to make such data available as downloadable TSVs, spreadsheets or similar formats. The author reagent table could also be incorporated into the evolvinguse of preprint repositories: an ART could simply be appended to the preprint manuscript. Feedback on this proposal from the larger biocuration community would be most welcome. Addendum: Genetics has now adopted the author reagent table; see their “Preparing Manuscripts for Submission” page. The template and example can be downloaded from flybase.org/journal/reagent_form. • In the form of a spreadsheet that can be used regularly during the course of a research project, recording reagents as they are used. • Would facilitate tracking within a lab. • If the same format is used for manuscript submissions, requires only minor editing on the part of the researcher. • Journals would receive reagent information in a format that is straightforward to handle and that allows downloads as TSV format or spreadsheet. • Wider use of identifiers and parsable formats would be a huge help for biological databases. • A widely used standardized formatwould facilitate propagation of accurate reagent information, allowing import of existing entries into a new table. Rows duplicated as needed (one row for each reagent). Row titles must remain unchanged; order can be changed; unused categories can be removed. Designed to facilitate automated parsing: Colors entirely optional and can be changed. Column order and titles must remain unchanged. Standardized template provided to researchers. Genetics and G3 are encouraging use of the Reagent Table. They are also solicitingfeedback from authors. Additional journals are being contacted. Opportunity to encourage use of RRIDs. (https://scicrunch.org/resources) We welcome feedback on this proposal, from researchers within and outside the model organism communities, from biocurators, and from any other interested parties. All feedback is helpful – whether detailed and specific, or more general. We are especially interested in additional data types that should be added. Please contact: Madeline (Lynn) Crosby [email protected] Multiple outstanding issues, for example: Should there be a dedicated column for RRIDs? (Would that discourage use of other identifiers?) Ideally, the use of standard identifiers would facilitate rigorous searches of the literature. This proposal does not address that issue, since a reagent table as part of supplementary information would not be visible to most text-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 Many thanks to members of ZFIN, SGD, WormBase, MGI, and the FlyBase SAB for input and thoughtful feedback.

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Page 1: Author Reagent Table: a proposal 70 - FlyBase · 2017. 4. 5. · Author Reagent Table: a proposal Madeline Crosby, Norbert Perrimon, and the FlyBase Consortium* Department of Molecular

AuthorReagentTable:aproposalMadelineCrosby,NorbertPerrimon,andtheFlyBaseConsortium*

DepartmentofMolecularandCellularBiology,HarvardUniversity

70

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.

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