Curation script for OBO Foundry ontology curators

README.md

The purpose of this script is to assist in connecting all contributors to OBO Foundry ontologies to Wikidata pages via their GitHub usernames. Here's a screencast of me explaining this and showing some demo curations: https://www.youtube.com/watch?v=ERJyrh7UIbg

Progress can be observed via the Wikidata Query Service by running the attached SPARQL query.

Typical curation workflow:

1. Look for GitHub users that are associated with a human name
2. Search ORCID to find their ORCID identifier
3. Use Scholia https://scholia.toolforge.org/orcid/ to see if their ORCID is linked to a Wikidata page
   • If not, it's pretty likely that there is no Wikidata page. Search the name in wikidata to be sure. Create an appropriate wikidata page, all you need to add is instance of human and the ORCID identifier
4. Add the GitHub username to the wikidata page

obofoundry_github_alignment.rq

SELECT DISTINCT ?github ?name ?person ?personLabel
WHERE
{
    VALUES (?github ?name) { 
        ("ANiknejad" "Anne Niknejad") ("AlanRace" "Alan Race") ("AmosBairoch" UNDEF) ("AnaReisCosta" UNDEF) ("Anoosha-Sehar" "Anoosha Sehar") ("AntonPetrov" "Anton Petrov") ("Antonarctica" UNDEF) ("Antonialock" "Antonia") ("Apujar" "Anu") ("Aqua1ung" "Cristian Cocos") ("Arlene-1998" "Arlene") ("Astghik-S" UNDEF) ("Audald" "Audald Lloret-Villas") ("BRENDA-Enzymes" "BRENDA Enzyme Database") ("BarbaraCzub" UNDEF) ("BideZ" "Bide Zhang") ("CDowland" "Clint Dowland") ("CMCosta" UNDEF) ("Clare72" UNDEF) ("ClusterDuck123" "ClusterDuck123") ("CooperStansbury" "Cooper Stansbury") ("CuzickA" UNDEF) ("DanBerrios" "Dan Berrios") ("Daniel-Mietchen" "Daniel Mietchen") ("Daniel-Olson" UNDEF) ("DiegoRegalado" UNDEF) ("DoctorBud" "Dan Keith") ("EliotRagueneau" "Eliot Ragueneau") ("EmilyBowlerBarnett" UNDEF) ("FernandaFarinelli" "Fernanda Farinelli") ("FrancescoVit" "Francesco Vitali") ("Hendricks27" "Wenjin") ("Huang-OMIT" "Jingshan Huang") ("Huffmaar" UNDEF) ("JArgasinska" UNDEF) ("JCGiron" "Jennifer C. Girón") ("JadeHotchkiss" UNDEF) ("Jguzman210" UNDEF) ("JohnLevander" "John ") ("JoshuaFortriede" UNDEF) ("Khuthalamnika" UNDEF) ("KrishnaTO" "Krishna Udaiwal") ("L-Leclere" UNDEF) ("LCCarmody" "Leigh Carmody") ("Lemon-Liu" "Liu Meng") ("LightGrenadier" UNDEF) ("LilyAndres" "Liliana Andres") ("MKonopko" UNDEF) ("Nobutake" UNDEF) ("OnToologyUser" "OnToologyUser") ("PaulNSchofield" UNDEF) ("RDruzinsky" "Robert Druzinsky") ("RalfG" "Ralf Gabriels") ("Rena-Yang-cell" "Rena Wang") ("S2Ola" "Olamidipupo Ajigboye") ("ShahimEssaid" "Shahim Essaid") ("Snowotarski" "Steph Nowotarski") ("Sohj" "Josh Hanna") ("StroemPhi" "Philip Strömert") ("Superraptor" "Clair Kronk") ("TGoepel" UNDEF) ("TaskeHAMANO" "Shinya Suzuki") ("ValWood" "Val Wood") ("WMBio" "mwang") ("ZH86" UNDEF) ("abretaud" "Anthony Bretaudeau") ("adbartni" "Alexander Bartnik") ("addiehl" "Alexander Diehl") ("aechchiki" "Amina Echchiki") ("aellenhicks" UNDEF) ("agbeltran" "Alejandra Gonzalez-Beltran") ("akodamullil" "Alpha Tom Kodamullil") ("alanruttenberg" "Alan Ruttenberg") ("alcpacaud" UNDEF) ("alexhenrie" "Alex Henrie") ("allenbaron" "J. Allen Baron") ("allysonlister" "Allyson Lister") ("althonos" "Martin Larralde") ("amalik01" UNDEF) ("amanjeev" "Amanjeev Sethi") ("ampeng" UNDEF) ("andrawaag" UNDEF) ("anitacaron" "Anita Caron") ("anna-anagnostop" "Anna V. Anagnostopoulos") ("annadunn3" UNDEF) ("annazhukova" "Anna Zhukova") ("annikalsmith" "Annika Smith") ("apmody" "Apurva Mody") ("ar-ibrahim" "arwa-ebi") ("arlin" "Arlin Stoltzfus") ("austinmeier" "Austin Meier") ("awqbi" UNDEF) ("b-sheppard" UNDEF) ("balhoff" "Jim Balhoff") ("batchelorc" "Colin Batchelor") ("bbopjenkins" UNDEF) ("bchisham" "Brandon Chisham") ("beckyjackson" "Becky Jackson") ("bgyori" "Benjamin M. Gyori") ("bittremieux" "Wout Bittremieux") ("bjonnh" "Jonathan Bisson") ("bkr-iotic" "Ben Reynolds") ("bobthacker" UNDEF) ("bonitalam" "Bonita Lam") ("bpeters42" UNDEF) ("brandonnodnarb" "brandonw") ("btsinn" "Brandon Sinn") ("bvarner-ebi" UNDEF) ("c15mnw" "Mike Wicks") ("caetera" UNDEF) ("callahantiff" "Tiffany J. Callahan") ("caripark" UNDEF) ("carlotorniai" "Carlo Torniai") ("carrineblank" "Carrine Blank") ("cbarcl01" UNDEF) ("cbielow" "Chris Bielow") ("cboelling" "Christian Bölling") ("ccadete" "ccadete") ("celineaubert" "Céline Aubert") ("cerivs" UNDEF) ("chambm" "Matt Chambers") ("chenchuming" "Chuming Chen") ("chris-grove" "Chris Grove") ("chumingc" UNDEF) ("cindyJax" UNDEF) ("citmejia" UNDEF) ("cjgrondin" UNDEF) ("cmrn-rhi" "Rhiannon Cameron") ("cmungall" "Chris Mungall") ("colinbatchelor" "Colin Batchelor") ("cooperl09" "Laurel Cooper") ("cosmicnet" "Lyle Hopkins") ("csparr" "Cyndy Sims Parr") ("cstoeckert" UNDEF) ("cthoyt" "Charles Tapley Hoyt") ("curious88323" UNDEF) ("cyamasak" "Chisato Yamasaki") ("cybersiddhu" "Siddhartha Basu") ("danielwelch" "Daniel Welch") ("daniwelter" UNDEF) ("davidwsant" "David Sant") ("dcambie" "dcambie") ("ddooley" "Damion Dooley") ("decorons" "Sherri de Coronado") ("deepakunni3" "Deepak") ("delphinedauga" UNDEF) ("dfornika" "Dan Fornika") ("dhimmel" "Daniel Himmelstein") ("diatomsRcool" UNDEF) ("dillerm" "Matthew Diller") ("dosumis" "David Osumi-Sutherland") ("dougli1sqrd" "Eric Douglass") ("dr-shorthair" "Simon Cox") ("drseb" "Sebastian Köhler") ("dsiegele" "Debby Siegele") ("dullhunk" "Duncan Hull") ("dustine32" UNDEF) ("e4ong1031" UNDEF) ("echinoderm-ontology" UNDEF) ("edeutsch" "Eric Deutsch") ("edwardsnj" "Nathan Edwards") ("egchristensen" "Evan Christensen") ("egonw" "Egon Willighagen") ("ehartley" "Emily Hartley") ("ejohnson1" UNDEF) ("elizabetharnaud" "Elizabeth Arnaud") ("elserj" UNDEF) ("elviram" "Elvira") ("emquardokus" UNDEF) ("epontell" "Enrico Pontelli") ("erindavies" UNDEF) ("ethierjf" UNDEF) ("euniceyi" UNDEF) ("fabiolib" "Fabio") ("fbastian" UNDEF) ("fjmanion" "Frank Manion") ("gdower" "Geoff Ower") ("germa" "Gerhard Mayer") ("getbordea" UNDEF) ("git4anjali" UNDEF) ("gjh34" UNDEF) ("gkoutos" "George Gkoutos") ("gmazandu" UNDEF) ("goodb" UNDEF) ("gooseberry11" UNDEF) ("gouttegd" "Damien Goutte-Gattat") ("grosscol" "Colin") ("haoyuanli" "Jimmy Li") ("harrisonstrachan" UNDEF) ("hdrabkin" "Harold Drabkin") ("hectorguzor" "Hector Guzman-Orozco") ("helenamachado" UNDEF) ("hjellis" "Helena Ellis") ("hkir-dev" "Huseyin Kir") ("hlapp" "Hilmar Lapp") ("hoganwr" "Bill Hogan") ("holger-stenzhorn" "Holger Stenzhorn") ("hrshdhgd" "Harshad") ("hstrachan" "Harrison Strachan") ("huangphil" UNDEF) ("hujo91" "Johannes Hunold") ("indiedotkim" "Joachim Kim Baran") ("ivansg44" UNDEF) ("iwilkie" "Isabella Wilkie") ("jaiswalp" "Pankaj Jaiswal") ("jamesaoverton" "James A. Overton") ("jamesmalone" "James Malone") ("janefarmstrong" UNDEF) ("janelomax" "Jane Lomax") ("jannahastings" "Janna Hastings") ("jar398" "Jonathan A Rees") ("jbmunro" "jbmunro") ("jdeck88" "John Deck") ("jdepons" UNDEF) ("jhammock" "Jen Hammock") ("jimhu-tamu" "Jim Hu") ("jmcmurry" "Julie McMurry") ("jmillanacosta" "Javier Millán Acosta") ("jmskip" UNDEF) ("jmwhorton" UNDEF) ("joeflack4" "Joe Flack") ("johannes-darms" "Johannes Darms") ("john-rincon" UNDEF) ("johnwjudkins" "John Judkins") ("jonathanbona" "Jonathan Bona") ("jonathanvajda" "Jonathan Vajda") ("joncison" "Jon Ison") ("jonrkarr" "Jonathan Karr") ("joshhanna" "Josh Hanna") ("jpgourdine" UNDEF) ("jroy4" "Joy Roy") ("jrsjrs" UNDEF) ("jseager7" "James Seager") ("jshofstahl" UNDEF) ("kaiiam" "Kai Blumberg") ("kallia-p" UNDEF) ("katiermullen" UNDEF) ("katrinleinweber" "Katrin Leinweber") ("kbdhaar" "Dharani Balasubramanian") ("kcranston" "Karen Cranston") ("keilbeck" "Karen EIlbeck") ("kenbabu" "kenneth") ("kevinschaper" "Kevin Schaper") ("kimrutherford" "Kim Rutherford") ("kingmanzhang" "Xingmin Aaron Zhang") ("kltm" "kltm") ("krchristie" "Karen R Christie") ("kristiholmes" "Kristi Holmes") ("kshefchek" "Kent Shefchek") ("kvillan" UNDEF) ("labda" "LaBDA") ("larrybabb" "Larry Babb") ("lauramoore1859" UNDEF) ("laurenechan" "Lauren") ("lbrensk" "Laura Brenskelle") ("leechuck" "Robert Hoehndorf") ("leonqli" UNDEF) ("lgcowell" UNDEF) ("lihuanbiti" UNDEF) ("linikujp" "Asiyah Yu Lin") ("lpaglione" "Laura Paglione") ("lpalbou" "lpalbou") ("lschriml" UNDEF) ("luanalicata" UNDEF) ("lubianat" "Tiago Lubiana") ("luciansmith" "Lucian Smith") ("luis-gonzalez-m" "Luis A. Gonzalez-Montaña") ("luizjoze" UNDEF) ("maestroe" UNDEF) ("mah11" "Midori Harris") ("manulera" "Manuel Lera Ramirez") ("marieALaporte" "Marie-Angélique Laporte") ("marijane" "marijane white") ("mark-jensen" "Mark Jensen") ("markengelstad" "Mark Engelstad") ("martinjramirez" "Martin J Ramirez") ("matentzn" "Nico Matentzoglu") ("mateolan" "Matthew Lange") ("matthiaskoenig" "Matthias König") ("mbrochhausen" "Mathias Brochhausen") ("mbrush" "Matthew Brush") ("mchibucos" "Marcus Chibucos, Ph.D.") ("mcourtot" "Melanie Courtot") ("megbalk" "Meghan Balk") ("meichen-liu" UNDEF) ("mellybelly" "Melissa Haendel") ("melodyswen" "Melody Swen") ("mfjackson" "Marty Jackson") ("mia-lgo" "Jimena Linares") ("micheldumontier" "Michel Dumontier") ("mjy" "Matt") ("mkeays" "Maria Keays") ("mmc46" "Marta Costa") ("mobiusklein" "Joshua Klein") ("momotsuyo" "Tsuyoshi") ("monadica" UNDEF) ("monicacecilia" "Monica Munoz-Torres") ("mshadbolt" "Marion") ("msinclair2" "Michael Sinclair") ("mtrobey" "Matt Robey") ("muntisa" "Cristian R Munteanu") ("muthuvenkat" "Venkatesh Muthukrishnan") ("mwalzer" "Mathias Walzer") ("nandadorea" "Nanda Dórea") ("narcijade" "Eric Ross") ("nataled" "Darren A. Natale") ("neilotte" "J. Neil Otte") ("ngrewe" "Niels Grewe") ("nicklondhe" "Nikhil Londhe") ("nicoleruiz" "Nicole Ruiz") ("nicolevasilevsky" "Nicole Vasilevsky") ("nlharris" "Nomi Harris") ("nlwashington" "Nicole Washington") ("nmcabili" UNDEF) ("noedelta" "Noemi del Toro Ayllón") ("nsewnath" "Neeka Sewnath") ("nsuvarnaiari" UNDEF) ("ntung" "Tung Nguyen") ("okoepler" UNDEF) ("olas" "Ola Spjuth") ("pabinz" UNDEF) ("paolaroncaglia" UNDEF) ("paulacalipho" "paulacalipho") ("paulbrowne" "Paul Browne") ("pbuttigieg" "Pier Luigi Buttigieg") ("pcastellanoescuder" "Pol Castellano Escuder") ("pellst" "Troy Pells") ("pfabry" UNDEF) ("pfey03" "Petra Fey") ("pgaudet" UNDEF) ("phwegner" "Philipp") ("pj3743" UNDEF) ("pmidford" "Peter E. Midford") ("pmt706" "Paul Thomas") ("pnrobinson" "Peter Robinson") ("pporrasebi" "Pablo Porras") ("proccaserra" "Philippe Rocca-Serra") ("proceps" "Dmitry Dmitriev") ("psyrebecca" "Suyuan Peng") ("raissameyer" "Raïssa Meyer") ("ramonawalls" "Ramona Walls") ("raphenya" "amos") ("raymond91105" UNDEF) ("raymond91125" "Raymond Lee") ("rays22" "Ray Stefancsik") ("rduerr" UNDEF) ("reality" "reality") ("renzok" "renzo") ("rfellers" "Ryan Fellers") ("rjdodson" UNDEF) ("rkboyce" "Richard D Boyce, PhD") ("robgur" "Rob") ("rosario-lombardo" UNDEF) ("rossmounce" "Ross Mounce") ("rsmsheriff" "Rahuman Sheriff") ("rtaseen" UNDEF) ("rudnicki" "Mateusz Rudnicki") ("rushtong" "Gregory Rushton") ("rvosa" "Rutger Vos") ("sabrinatoro" UNDEF) ("safisher" UNDEF) ("sagehrke" "Sarah Gehrke") ("sbello" "Sue Bello") ("sbjain" UNDEF) ("scdodev" UNDEF) ("schaferw" UNDEF) ("scheuerm" "Richard Scheuermann") ("scottcain" "Scott Cain") ("sdumitriu" "Sergiu Dumitriu") ("seger" "Erik Segerdell") ("seljaseppala" "Selja Seppälä") ("sergeitarasov" "Sergei Tarasov") ("seymourmegan" "Megan Seymour") ("sgebel" UNDEF) ("shawntanzk" "Shawn Tan") ("shwolfish" UNDEF) ("sierra-moxon" "Sierra Moxon") ("siiraa" "Sirarat Sarntivijai") ("simonjupp" "Simon Jupp") ("sjbost" "Sarah Bost") ("snacktavish" "Emily Jane McTavish") ("sneumann" "Steffen Neumann") ("solideoglori" "Jonathan Lawson") ("srobb1" "Sofia Robb") ("srynobio" "Shawn Rynearson") ("stain" "Stian Soiland-Reyes") ("steschu63" UNDEF) ("stevenchong" "Steven Chong") ("stuckyb" UNDEF) ("suzialeksander" UNDEF) ("tamuzhou" UNDEF) ("tberardini" "Tanya Berardini") ("teleaslamellatus" UNDEF) ("temjones" "Tamsin Jones") ("tfhayamizu" UNDEF) ("tgbugs" "Tom Gillespie") ("theisuru" "Isuru Liyanage") ("thomaspd" UNDEF) ("timosachsenberg" "Timo Sachsenberg") ("tnavatar" UNDEF) ("tonysawfordebi" "Tony Sawford") ("tucotuco" "John Wieczorek") ("turbomam" "Mark A. Miller") ("tutajm" "Marek Tutaj") ("ubyndr" "Ismail Ugur Bayindir") ("ukaraoz" UNDEF) ("ukemi" "David Hill") ("utecht" "Joseph Utecht") ("vanaukenk" UNDEF) ("vasvir" "Vassilis Virvilis") ("vhtierrafria" UNDEF) ("vtoure" "Vasundra Touré") ("wawong" "Willy Wong") ("wdahdul" "Wasila Dahdul") ("wdduncan" "Bill Duncan") ("wildlifehexagon" "Eric Hartline") ("wilsontom" "Tom Wilson") ("ybradford" UNDEF) ("yingtliu" UNDEF) ("yongqunh" "Yongqun Oliver He") ("ypandit" "Yogesh Pandit") ("ypriverol" "Yasset Perez-Riverol") ("yuki-yamagata" "Yuki") ("yy20716" "HyeongSik Kim") ("zachll" UNDEF) ("zdwrkacct" UNDEF) ("zhengj2007" "jie zheng") ("zhilianghu" "Zhiliang Hu") ("zhiliangme" "Zhiliang Hu") ("zoependlington" "Zoë May Pendlington") 
    }
    OPTIONAL {
        ?person wdt:P2037 ?github .
        OPTIONAL { ?person wdt:P496 ?orcid }
    }
    SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}