The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.

Putman TE, Schaper K, Matentzoglu N, Rubinetti VP, Alquaddoomi FS, Cox C, Caufield JH, Elsarboukh G, Gehrke S, Hegde H, Reese JT, Braun I, Bruskiewich RM, Cappelletti L, Carbon S, Caron AR, Chan LE, Chute CG, Cortes KG, De Souza V, Fontana T, Harris NL, Hartley EL, Hurwitz E, Jacobsen JOB, Krishnamurthy M, Laraway BJ, McLaughlin JA, McMurry JA, Moxon SAT, Mullen KR, O'Neil ST, Shefchek KA, Stefancsik R, Toro S, Vasilevsky NA, Walls RL, Whetzel PL, Osumi-Sutherland D, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC.

Nucleic Acids Res, 2024

doi:10.1093/nar/gkad1082.

Expression Atlas update: insights from sequencing data at both bulk and single cell level.

George N, Fexova S, Fuentes AM, Madrigal P, Bi Y, Iqbal H, Kumbham U, Nolte NF, Zhao L, Thanki AS, Yu ID, Marugan Calles JC, Erdos K, Vilmovsky L, Kurri SR, Vathrakokoili-Pournara A, Osumi-Sutherland D, Prakash A, Wang S, Tello-Ruiz MK, Kumari S, Ware D, Goutte-Gattat D, Hu Y, Brown N, Perrimon N, Vizcaíno JA, Burdett T, Teichmann S, Brazma A, Papatheodorou I.

Nucleic Acids Res, 2024

doi:10.1093/nar/gkad1021.

A guide to the BRAIN Initiative Cell Census Network data ecosystem.

Hawrylycz M, Martone ME, Ascoli GA, Bjaalie JG, Dong HW, Ghosh SS, Gillis J, Hertzano R, Haynor DR, Hof PR, Kim Y, Lein E, Liu Y, Miller JA, Mitra PP, Mukamel E, Ng L, Osumi-Sutherland D, Peng H, Ray PL, Sanchez R, Regev A, Ropelewski A, Scheuermann RH, Tan SZK, Thompson CL, Tickle T, Tilgner H, Varghese M, Wester B, White O, Zeng H, Aevermann B, Allemang D, Ament S, Athey TL, Baker C, Baker KS, Baker PM, Bandrowski A, Banerjee S, Bishwakarma P, Carr A, Chen M, Choudhury R, Cool J, Creasy H, D'Orazi F, Degatano K, Dichter B, Ding SL, Dolbeare T, Ecker JR, Fang R, Fillion-Robin JC, Fliss TP, Gee J, Gillespie T, Gouwens N, Zhang GQ, Halchenko YO, Harris NL, Herb BR, Hintiryan H, Hood G, Horvath S, Huo B, Jarecka D, Jiang S, Khajouei F, Kiernan EA, Kir H, Kruse L, Lee C, Lelieveldt B, Li Y, Liu H, Liu L, Markuhar A, Mathews J, Mathews KL, Mezias C, Miller MI, Mollenkopf T, Mufti S, Mungall CJ, Orvis J, Puchades MA, Qu L, Receveur JP, Ren B, Sjoquist N, Staats B, Tward D, van Velthoven CTJ, Wang Q, Xie F, Xu H, Yao Z, Yun Z, Zhang YR, Zheng WJ, Zingg B.

PLoS Biol, 2023

doi:10.1371/journal.pbio.3002133.

Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics.

Girón JC, Tarasov S, González Montaña LA, Matentzoglu N, Smith AD, Koch M, Boudinot BE, Bouchard P, Burks R, Vogt L, Yoder M, Osumi-Sutherland D, Friedrich F, Beutel RG, Mikó I.

Syst Biol, 2023

doi:10.1093/sysbio/syad025.

The Ontology of Biological Attributes (OBA)-computational traits for the life sciences.

Stefancsik R, Balhoff JP, Balk MA, Ball RL, Bello SM, Caron AR, Chesler EJ, de Souza V, Gehrke S, Haendel M, Harris LW, Harris NL, Ibrahim A, Koehler S, Matentzoglu N, McMurry JA, Mungall CJ, Munoz-Torres MC, Putman T, Robinson P, Smedley D, Sollis E, Thessen AE, Vasilevsky N, Walton DO, Osumi-Sutherland D.

Mamm Genome, 2023

doi:10.1007/s00335-023-09992-1.

Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas.

Herr BW, Hardi J, Quardokus EM, Bueckle A, Chen L, Wang F, Caron AR, Osumi-Sutherland D, Musen MA, Börner K.

Sci Data, 2023

doi:10.1038/s41597-023-01993-8.

Virtual Fly Brain-An interactive atlas of the <i>Drosophila</i> nervous system.

Court R, Costa M, Pilgrim C, Millburn G, Holmes A, McLachlan A, Larkin A, Matentzoglu N, Kir H, Parkinson H, Brown NH, O'Kane CJ, Armstrong JD, Jefferis GSXE, Osumi-Sutherland D.

Front Physiol, 2023

doi:10.3389/fphys.2023.1076533.

Brain Data Standards - A method for building data-driven cell-type ontologies.

Tan SZK, Kir H, Aevermann BD, Gillespie T, Harris N, Hawrylycz MJ, Jorstad NL, Lein ES, Matentzoglu N, Miller JA, Mollenkopf TS, Mungall CJ, Ray PL, Sanchez REA, Staats B, Vermillion J, Yadav A, Zhang Y, Scheuermann RH, Osumi-Sutherland D.

Sci Data, 2023

doi:10.1038/s41597-022-01886-2.

COVoc and COVTriage: novel resources to support literature triage.

Caucheteur D, May Pendlington Z, Roncaglia P, Gobeill J, Mottin L, Matentzoglu N, Agosti D, Osumi-Sutherland D, Parkinson H, Ruch P.

Bioinformatics, 2023

doi:10.1093/bioinformatics/btac800.

The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource.

Sollis E, Mosaku A, Abid A, Buniello A, Cerezo M, Gil L, Groza T, Güneş O, Hall P, Hayhurst J, Ibrahim A, Ji Y, John S, Lewis E, MacArthur JAL, McMahon A, Osumi-Sutherland D, Panoutsopoulou K, Pendlington Z, Ramachandran S, Stefancsik R, Stewart J, Whetzel P, Wilson R, Hindorff L, Cunningham F, Lambert SA, Inouye M, Parkinson H, Harris LW.

Nucleic Acids Res, 2023

doi:10.1093/nar/gkac1010.

The BRAIN Initiative Cell Census Network Data Ecosystem: A User’s Guide

BICCN Data Ecosystem Collaboration, Hawrylycz MJ, Martone ME, Hof PR, Lein ES, Regev A, Ascoli GAA, Bjaalie JG, Dong H, Ghosh SS, Gillis J, Hertzano R, Haynor DR, Kim Y, Liu Y, Miller JA, Mitra PP, Mukamel E, Osumi-Sutherland D, Peng H, Ray PL, Sanchez R, Ropelewski A, Scheuermann RH, Tan SZK, Tickle T, Tilgner H, Varghese M, Wester B, White O, Aevermann B, Allemang D, Ament S, Athey TL, Baker PM, Baker C, Baker KS, Bandrowski A, Bishwakarma P, Carr A, Chen M, Choudhury R, Cool J, Creasy H, D'Orazi F, Degatano K, Dichter B, Ding S, Dolbeare T, Ecker JR, Fang R, Fillion-Robin J, Fliss TP, Gee J, Gillespie T, Gouwens N, Halchenko YO, Harris N, Herb BR, Hintiryan H, Hood G, Horvath S, Jarecka D, Jiang S, Khajouei F, Kiernan EA, Kir H, Kruse L, Lee C, Lelieveldt B, Li Y, Liu H, Markuhar A, Mathews J, Mathews KL, Miller MI, Mollenkopf T, Mufti S, Mungall CJ, Ng L, Orvis J, Puchades MA, Qu L, Receveur JP, Ren B, Sjoquist N, Staats B, Thompson CL, Tward D, van Velthoven CTJ, Wang Q, Xie F, Xu H, Yao Z, Yun Z, Zeng H, Zhang G, Zhang YR, Zheng JW, Zingg B.

2022

doi:10.1101/2022.10.26.513573.

Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies.

Matentzoglu N, Goutte-Gattat D, Tan SZK, Balhoff JP, Carbon S, Caron AR, Duncan WD, Flack JE, Haendel M, Harris NL, Hogan WR, Hoyt CT, Jackson RC, Kim H, Kir H, Larralde M, McMurry JA, Overton JA, Peters B, Pilgrim C, Stefancsik R, Robb SM, Toro S, Vasilevsky NA, Walls R, Mungall CJ, Osumi-Sutherland D.

Database (Oxford), 2022

doi:10.1093/database/baac087.

Specimen, Biological Structure, and Spatial Ontologies in Support of a Human Reference Atlas

Herr BW, Hardi J, Quardokus EM, Bueckle A, Chen L, Wang F, Caron AR, Osumi-Sutherland D, Musen MA, Börner K.

2022

doi:10.1101/2022.09.08.507220.

A Simple Standard for Sharing Ontological Mappings (SSSOM).

Matentzoglu N, Balhoff JP, Bello SM, Bizon C, Brush M, Callahan TJ, Chute CG, Duncan WD, Evelo CT, Gabriel D, Graybeal J, Gray A, Gyori BM, Haendel M, Harmse H, Harris NL, Harrow I, Hegde HB, Hoyt AL, Hoyt CT, Jiao D, Jiménez-Ruiz E, Jupp S, Kim H, Koehler S, Liener T, Long Q, Malone J, McLaughlin JA, McMurry JA, Moxon S, Munoz-Torres MC, Osumi-Sutherland D, Overton JA, Peters B, Putman T, Queralt-Rosinach N, Shefchek K, Solbrig H, Thessen A, Tudorache T, Vasilevsky N, Wagner AH, Mungall CJ.

Database (Oxford), 2022

doi:10.1093/database/baac035.

Mondo: Unifying diseases for the world, by the world

Vasilevsky NA, Matentzoglu NA, Toro S, Flack JE, Hegde H, Unni DR, Alyea GF, Amberger JS, Babb L, Balhoff JP, Bingaman TI, Burns GA, Buske OJ, Callahan TJ, Carmody LC, Cordo PC, Chan LE, Chang GS, Christiaens SL, Dumontier M, Failla LE, Flowers MJ, Garrett HA, Goldstein JL, Gration D, Groza T, Hanauer M, Harris NL, Hilton JA, Himmelstein DS, Hoyt CT, Kane MS, Köhler S, Lagorce D, Lai A, Larralde M, Lock A, López Santiago I, Maglott DR, Malheiro AJ, Meldal BHM, Munoz-Torres MC, Nelson TH, Nicholas FW, Ochoa D, Olson DP, Oprea TI, Osumi-Sutherland D, Parkinson H, Pendlington ZM, Rath A, Rehm HL, Remennik L, Riggs ER, Roncaglia P, Ross JE, Shadbolt MF, Shefchek KA, Similuk MN, Sioutos N, Smedley D, Sparks R, Stefancsik R, Stephan R, Storm AL, Stupp D, Stupp GS, Sundaramurthi JC, Tammen I, Tay D, Thaxton CL, Valasek E, Valls-Margarit J, Wagner AH, Welter D, Whetzel PL, Whiteman LL, Wood V, Xu CH, Zankl A, Zhang XA, Chute CG, Robinson PN, Mungall CJ, Hamosh A, Haendel MA.

2022

doi:10.1101/2022.04.13.22273750.

The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.

Fisher ME, Segerdell E, Matentzoglu N, Nenni MJ, Fortriede JD, Chu S, Pells TJ, Osumi-Sutherland D, Chaturvedi P, James-Zorn C, Sundararaj N, Lotay VS, Ponferrada V, Wang DZ, Kim E, Agalakov S, Arshinoff BI, Karimi K, Vize PD, Zorn AM.

BMC Bioinformatics, 2022

doi:10.1186/s12859-022-04636-8.

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.

Li H, Janssens J, De Waegeneer M, Kolluru SS, Davie K, Gardeux V, Saelens W, David FPA, Brbić M, Spanier K, Leskovec J, McLaughlin CN, Xie Q, Jones RC, Brueckner K, Shim J, Tattikota SG, Schnorrer F, Rust K, Nystul TG, Carvalho-Santos Z, Ribeiro C, Pal S, Mahadevaraju S, Przytycka TM, Allen AM, Goodwin SF, Berry CW, Fuller MT, White-Cooper H, Matunis EL, DiNardo S, Galenza A, O'Brien LE, Dow JAT, FCA Consortium§, Jasper H, Oliver B, Perrimon N, Deplancke B, Quake SR, Luo L, Aerts S, Agarwal D, Ahmed-Braimah Y, Arbeitman M, Ariss MM, Augsburger J, Ayush K, Baker CC, Banisch T, Birker K, Bodmer R, Bolival B, Brantley SE, Brill JA, Brown NC, Buehner NA, Cai XT, Cardoso-Figueiredo R, Casares F, Chang A, Clandinin TR, Crasta S, Desplan C, Detweiler AM, Dhakan DB, Donà E, Engert S, Floc'hlay S, George N, González-Segarra AJ, Groves AK, Gumbin S, Guo Y, Harris DE, Heifetz Y, Holtz SL, Horns F, Hudry B, Hung RJ, Jan YN, Jaszczak JS, Jefferis GSXE, Karkanias J, Karr TL, Katheder NS, Kezos J, Kim AA, Kim SK, Kockel L, Konstantinides N, Kornberg TB, Krause HM, Labott AT, Laturney M, Lehmann R, Leinwand S, Li J, Li JSS, Li K, Li K, Li L, Li T, Litovchenko M, Liu HH, Liu Y, Lu TC, Manning J, Mase A, Matera-Vatnick M, Matias NR, McDonough-Goldstein CE, McGeever A, McLachlan AD, Moreno-Roman P, Neff N, Neville M, Ngo S, Nielsen T, O'Brien CE, Osumi-Sutherland D, Özel MN, Papatheodorou I, Petkovic M, Pilgrim C, Pisco AO, Reisenman C, Sanders EN, Dos Santos G, Scott K, Sherlekar A, Shiu P, Sims D, Sit RV, Slaidina M, Smith HE, Sterne G, Su YH, Sutton D, Tamayo M, Tan M, Tastekin I, Treiber C, Vacek D, Vogler G, Waddell S, Wang W, Wilson RI, Wolfner MF, Wong YE, Xie A, Xu J, Yamamoto S, Yan J, Yao Z, Yoda K, Zhu R, Zinzen RP.

Science, 2022

doi:10.1126/science.abk2432.

Formalizing Insect Morphological Data: A Model-Based, Extensible Insect Anatomy Ontology and Its Potential Applications in Biodiversity Research and Informatics

Girón JC, Tarasov S, González Montaña LA, Matentzoglu N, Smith AD, Koch M, Boudinot BE, Bouchard P, Burks R, Vogt L, Yoder M, Osumi-Sutherland D, Friedrich F, Beutel R, Mikó I.

2022

doi:10.20944/preprints202201.0254.v1.

Expression Atlas update: gene and protein expression in multiple species.

Moreno P, Fexova S, George N, Manning JR, Miao Z, Mohammed S, Muñoz-Pomer A, Fullgrabe A, Bi Y, Bush N, Iqbal H, Kumbham U, Solovyev A, Zhao L, Prakash A, García-Seisdedos D, Kundu DJ, Wang S, Walzer M, Clarke L, Osumi-Sutherland D, Tello-Ruiz MK, Kumari S, Ware D, Eliasova J, Arends MJ, Nawijn MC, Meyer K, Burdett T, Marioni J, Teichmann S, Vizcaíno JA, Brazma A, Papatheodorou I.

Nucleic Acids Res, 2022

doi:10.1093/nar/gkab1030.

Anatomical structures, cell types and biomarkers of the Human Reference Atlas.

Börner K, Teichmann SA, Quardokus EM, Gee JC, Browne K, Osumi-Sutherland D, Herr BW, Bueckle A, Paul H, Haniffa M, Jardine L, Bernard A, Ding SL, Miller JA, Lin S, Halushka MK, Boppana A, Longacre TA, Hickey J, Lin Y, Valerius MT, He Y, Pryhuber G, Sun X, Jorgensen M, Radtke AJ, Wasserfall C, Ginty F, Ho J, Sunshine J, Beuschel RT, Brusko M, Lee S, Malhotra R, Jain S, Weber G.

Nat Cell Biol, 2021

doi:10.1038/s41556-021-00788-6.

Cell type ontologies of the Human Cell Atlas.

Osumi-Sutherland D, Xu C, Keays M, Levine AP, Kharchenko PV, Regev A, Lein E, Teichmann SA.

Nat Cell Biol, 2021

doi:10.1038/s41556-021-00787-7.

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.

Jackson R, Matentzoglu N, Overton JA, Vita R, Balhoff JP, Buttigieg PL, Carbon S, Courtot M, Diehl AD, Dooley DM, Duncan WD, Harris NL, Haendel MA, Lewis SE, Natale DA, Osumi-Sutherland D, Ruttenberg A, Schriml LM, Smith B, Stoeckert CJ, Vasilevsky NA, Walls RL, Zheng J, Mungall CJ, Peters B.

Database (Oxford), 2021

doi:10.1093/database/baab069.

Brain Data Standards - A method for building data-driven cell-type ontologies

Tan SZK, Kir H, Aevermann BD, Gillespie T, Harris N, Hawrylycz M, Jorstad N, Lein E, Matentzoglu N, Miller JA, Mollenkopf TS, Mungall CJ, Ray PL, Sanchez REA, Staats B, Vermillion J, Yadav A, Zhang Y, Scheuermann RH, Osumi-Sutherland D.

2021

doi:10.1101/2021.10.10.463703.

Fly Cell Atlas: a single-cell transcriptomic atlas of the adult fruit fly

Li H, Janssens J, De Waegeneer M, Kolluru SS, Davie K, Gardeux V, Saelens W, David F, Brbić M, Leskovec J, McLaughlin CN, Xie Q, Jones RC, Brueckner K, Shim J, Tattikota SG, Schnorrer F, Rust K, Nystul TG, Carvalho-Santos Z, Ribeiro C, Pal S, Przytycka TM, Allen AM, Goodwin SF, Berry CW, Fuller MT, White-Cooper H, Matunis EL, DiNardo S, Galenza A, O’Brien LE, Dow JAT, Jasper H, Oliver B, Perrimon N, Deplancke B, Quake SR, Luo L, Aerts S, FCA Consortium.

2021

doi:10.1101/2021.07.04.451050.

OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies

Jackson RC, Matentzoglu N, Overton JA, Vita R, Balhoff JP, Buttigieg PL, Carbon S, Courtot M, Diehl AD, Dooley D, Duncan W, Harris NL, Haendel MA, Lewis SE, Natale DA, Osumi-Sutherland D, Ruttenberg A, Schriml LM, Smith B, Stoeckert CJ, Vasilevsky NA, Walls RL, Zheng J, Mungall CJ, Peters B.

2021

doi:10.1101/2021.06.01.446587.

Anatomical Structures, Cell Types, and Biomarkers Tables Plus 3D Reference Organs in Support of a Human Reference Atlas

Börner K, Teichmann SA, Quardokus EM, Gee J, Browne K, Osumi-Sutherland D, Herr BW, Bueckle A, Paul H, Haniffa MA, Jardine L, Bernard A, Ding S, Miller JA, Lin S, Halushka M, Boppana A, Longacre TA, Hickey J, Lin Y, Valerius MT, He Y, Pryhuber G, Sun X, Jorgensen M, Radtke AJ, Wasserfall C, Ginty F, Ho J, Sunshine J, Beuschel RT, Brusko M, Lee S, Malhotra R, Jain S, Weber G.

2021

doi:10.1101/2021.05.31.446440.

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.

Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Della Rocca M, Dunn N, Essaid S, Fey P, Grove C, Gourdine JP, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, Köhler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D.

Nucleic Acids Res, 2020

doi:10.1093/nar/gkz997.

Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems.

Thomas PD, Hill DP, Mi H, Osumi-Sutherland D, Van Auken K, Carbon S, Balhoff JP, Albou LP, Good B, Gaudet P, Lewis SE, Mungall CJ.

Nat Genet, 2019

doi:10.1038/s41588-019-0500-1.

SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse.

Koopmans F, van Nierop P, Andres-Alonso M, Byrnes A, Cijsouw T, Coba MP, Cornelisse LN, Farrell RJ, Goldschmidt HL, Howrigan DP, Hussain NK, Imig C, de Jong APH, Jung H, Kohansalnodehi M, Kramarz B, Lipstein N, Lovering RC, MacGillavry H, Mariano V, Mi H, Ninov M, Osumi-Sutherland D, Pielot R, Smalla KH, Tang H, Tashman K, Toonen RFG, Verpelli C, Reig-Viader R, Watanabe K, van Weering J, Achsel T, Ashrafi G, Asi N, Brown TC, De Camilli P, Feuermann M, Foulger RE, Gaudet P, Joglekar A, Kanellopoulos A, Malenka R, Nicoll RA, Pulido C, de Juan-Sanz J, Sheng M, Südhof TC, Tilgner HU, Bagni C, Bayés À, Biederer T, Brose N, Chua JJE, Dieterich DC, Gundelfinger ED, Hoogenraad C, Huganir RL, Jahn R, Kaeser PS, Kim E, Kreutz MR, McPherson PS, Neale BM, O'Connor V, Posthuma D, Ryan TA, Sala C, Feng G, Hyman SE, Thomas PD, Smit AB, Verhage M.

Neuron, 2019

doi:10.1016/j.neuron.2019.05.002.

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.

Köhler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine JP, Gargano M, Harris NL, Matentzoglu N, McMurry JA, Osumi-Sutherland D, Cipriani V, Balhoff JP, Conlin T, Blau H, Baynam G, Palmer R, Gratian D, Dawkins H, Segal M, Jansen AC, Muaz A, Chang WH, Bergerson J, Laulederkind SJF, Yüksel Z, Beltran S, Freeman AF, Sergouniotis PI, Durkin D, Storm AL, Hanauer M, Brudno M, Bello SM, Sincan M, Rageth K, Wheeler MT, Oegema R, Lourghi H, Della Rocca MG, Thompson R, Castellanos F, Priest J, Cunningham-Rundles C, Hegde A, Lovering RC, Hajek C, Olry A, Notarangelo L, Similuk M, Zhang XA, Gómez-Andrés D, Lochmüller H, Dollfus H, Rosenzweig S, Marwaha S, Rath A, Sullivan K, Smith C, Milner JD, Leroux D, Boerkoel CF, Klion A, Carter MC, Groza T, Smedley D, Haendel MA, Mungall C, Robinson PN.

Nucleic Acids Res, 2019

doi:10.1093/nar/gky1105.

Big data and single cell transcriptomics: implications for ontological representation

Aevermann BD, Novotny M, Bakken T, Miller JA, Diehl AD, Osumi-Sutherland D, Lasken RS, Lein ES, Scheuermann RH.

2018

doi:10.1101/257352.

Cell type discovery using single-cell transcriptomics: implications for ontological representation.

Aevermann BD, Novotny M, Bakken T, Miller JA, Diehl AD, Osumi-Sutherland D, Lasken RS, Lein ES, Scheuermann RH.

Hum Mol Genet, 2018

doi:10.1093/hmg/ddy100.

Using OWL reasoning to support the generation of novel gene sets for enrichment analysis.

Osumi-Sutherland DJ, Ponta E, Courtot M, Parkinson H, Badi L.

J Biomed Semantics, 2018

doi:10.1186/s13326-018-0175-z.

Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology.

Lovering RC, Roncaglia P, Howe DG, Laulederkind SJF, Khodiyar VK, Berardini TZ, Tweedie S, Foulger RE, Osumi-Sutherland D, Campbell NH, Huntley RP, Talmud PJ, Blake JA, Breckenridge R, Riley PR, Lambiase PD, Elliott PM, Clapp L, Tinker A, Hill DP.

Circ Genom Precis Med, 2018

doi:10.1161/circgen.117.001813.

Cell ontology in an age of data-driven cell classification.

Osumi-Sutherland D.

BMC Bioinformatics, 2017

doi:10.1186/s12859-017-1980-6.

Dead simple OWL design patterns.

Osumi-Sutherland D, Courtot M, Balhoff JP, Mungall C.

J Biomed Semantics, 2017

doi:10.1186/s13326-017-0126-0.

Bacterial Virus Ontology; Coordinating across Databases.

Hulo C, Masson P, Toussaint A, Osumi-Sutherland D, de Castro E, Auchincloss AH, Poux S, Bougueleret L, Xenarios I, Le Mercier P.

Viruses, 2017

doi:10.3390/v9060126.

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, He Y, Osumi-Sutherland D, Ruttenberg A, Sarntivijai S, Van Slyke CE, Vasilevsky NA, Haendel MA, Blake JA, Mungall CJ.

J Biomed Semantics, 2016

doi:10.1186/s13326-016-0088-7.

PhenoImageShare: an image annotation and query infrastructure.

Adebayo S, McLeod K, Tudose I, Osumi-Sutherland D, Burdett T, Baldock R, Burger A, Parkinson H.

J Biomed Semantics, 2016

doi:10.1186/s13326-016-0072-2.

Guidelines for the functional annotation of microRNAs using the Gene Ontology.

Huntley RP, Sitnikov D, Orlic-Milacic M, Balakrishnan R, D'Eustachio P, Gillespie ME, Howe D, Kalea AZ, Maegdefessel L, Osumi-Sutherland D, Petri V, Smith JR, Van Auken K, Wood V, Zampetaki A, Mayr M, Lovering RC.

RNA, 2016

doi:10.1261/rna.055301.115.

Representing virus-host interactions and other multi-organism processes in the Gene Ontology.

Foulger RE, Osumi-Sutherland D, McIntosh BK, Hulo C, Masson P, Poux S, Le Mercier P, Lomax J.

BMC Microbiol, 2015

doi:10.1186/s12866-015-0481-x.

Finding our way through phenotypes.

Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P.

PLoS Biol, 2015

doi:10.1371/journal.pbio.1002033.

Gene Ontology Consortium: going forward.

Gene Ontology Consortium.

Nucleic Acids Res, 2015

doi:10.1093/nar/gku1179.

Virtual Fly Brain - Using OWL to support the mapping and genetic dissection of the <i>Drosophila</i> brain.

Osumi-Sutherland D, Costa M, Court R, O'Kane CJ.

CEUR Workshop Proc, 2014

doi:.

Use of OWL within the Gene Ontology

Mungall CJ, Dietze H, Osumi-Sutherland D.

2014

doi:10.1101/010090.

TermGenie - a web-application for pattern-based ontology class generation.

Dietze H, Berardini TZ, Foulger RE, Hill DP, Lomax J, Osumi-Sutherland D, Roncaglia P, Mungall CJ.

J Biomed Semantics, 2014

doi:10.1186/2041-1480-5-48.

Meeting report: advancing practical applications of biodiversity ontologies

Walls R, Guralnick R, Deck J, Buntzman A, Buttigieg P, Davies N, Denslow M, Gallery R, Parnell J, Osumi-Sutherland D, Robbins R, Rocca-Serra P, Wieczorek J, Zheng J.

Stand Genomic Sci, 2014

doi:10.1186/1944-3277-9-17.

Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.

Dahdul WM, Cui H, Mabee PM, Mungall CJ, Osumi-Sutherland D, Walls RL, Haendel MA.

J Biomed Semantics, 2014

doi:10.1186/2041-1480-5-34.

The Drosophila anatomy ontology.

Costa M, Reeve S, Grumbling G, Osumi-Sutherland D.

J Biomed Semantics, 2013

doi:10.1186/2041-1480-4-32.

The Drosophila phenotype ontology.

Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Falls K, Brown NH, Gkoutos GV.

J Biomed Semantics, 2013

doi:10.1186/2041-1480-4-30.

Systematic analysis of experimental phenotype data reveals gene functions.

Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV.

PLoS One, 2013

doi:10.1371/journal.pone.0060847.

FlyBase: improvements to the bibliography.

Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ, FlyBase consortium.

Nucleic Acids Res, 2013

doi:10.1093/nar/gks1024.

Opportunities for text mining in the FlyBase genetic literature curation workflow.

McQuilton P, FlyBase Consortium.

Database (Oxford), 2012

doi:10.1093/database/bas039.

Directly e-mailing authors of newly published papers encourages community curation.

Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH, FlyBase Consortium.

Database (Oxford), 2012

doi:10.1093/database/bas024.

A strategy for building neuroanatomy ontologies.

Osumi-Sutherland D, Reeve S, Mungall CJ, Neuhaus F, Ruttenberg A, Jefferis GS, Armstrong JD.

Bioinformatics, 2012

doi:10.1093/bioinformatics/bts113.

The Virtual Fly Brain browser and query interface.

Milyaev N, Osumi-Sutherland D, Reeve S, Burton N, Baldock RA, Armstrong JD.

Bioinformatics, 2012

doi:10.1093/bioinformatics/btr677.

FlyBase 101--the basics of navigating FlyBase.

McQuilton P, St Pierre SE, Thurmond J, FlyBase Consortium.

Nucleic Acids Res, 2012

doi:10.1093/nar/gkr1030.

FlyBase: enhancing Drosophila Gene Ontology annotations.

Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi-Sutherland D, Schroeder A, Seal R, Zhang H, FlyBase Consortium.

Nucleic Acids Res, 2009

doi:10.1093/nar/gkn788.

Lab chiefs fear European rules will cost postdoc jobs.

Osumi-Sutherland D.

Nature, 2004

doi:10.1038/431006b.

Sick veterans pin hopes on Gulf War inquiry.

Osumi-Sutherland D.

Nature, 2004

doi:10.1038/430821a.