2025
Image-Based Search in Radiology: Identification of Brain Tumor Subtypes within Databases Using MRI-Based Radiomic Features.
von Reppert M, Chadha S, Willms K, Avesta A, Maleki N, Zeevi T, Lost J, Tillmanns N, Jekel L, Merkaj S, Lin M, Hoffmann K, Aneja S, Aboian M. Image-Based Search in Radiology: Identification of Brain Tumor Subtypes within Databases Using MRI-Based Radiomic Features. American Journal Of Neuroradiology 2025, 46: 1421-1428. PMID: 40250848, DOI: 10.3174/ajnr.a8805.Peer-Reviewed Original ResearchConceptsDimensionality reduction techniquesQuery caseImage search enginesImage-based searchReduction techniquesQuery subsetsRetrieval performanceQuery onesDimensionality reductionVisual similarityQuerySearch enginesSearch approachSearch methodTumor segmentationImage-basedRadiomic featuresNearest neighborsTumor typesDimensionalityBrain tumorsData setsNinety-five patientsLikert scoresMRI-based radiomic features
2023
Utility of an Artificial Intelligence Language Model for Post-Operative Patient Instructions Following Facial Trauma
Mohan S, Souza S, Fakurnejad S, Knott P. Utility of an Artificial Intelligence Language Model for Post-Operative Patient Instructions Following Facial Trauma. Craniomaxillofacial Trauma & Reconstruction 2023, 17: 291-294. PMID: 39634572, PMCID: PMC11613249, DOI: 10.1177/19433875231222803.Peer-Reviewed Original ResearchElectronic medical recordsPost-operative instructionsElectronic medical record templatesGoogle search enginePatient Education Materials Assessment ToolFacial traumaTrauma proceduresPEMAT-PProcedure-specific scoresUnderstanding scoresAssessment toolPatient instructionsMedical recordsSearch enginesAction scoresScoresTailored instructionOn bridging consumer health search across languages using cross-lingual word space
Chang C, Yang C. On bridging consumer health search across languages using cross-lingual word space. Electronic Commerce Research And Applications 2023, 59: 101254. DOI: 10.1016/j.elerap.2023.101254.Peer-Reviewed Original ResearchConsumer health searchInformation retrieval moduleRetrieval moduleRetrieval performanceHealth searchesWord spaceWeakly-supervised approachInformation search enginesHealth informationSeeking health informationRetrieval frameworkRetrieval tasksElectronic commerceMedical expressionsSearch enginesHealth vocabularyConstruction moduleInformation searchTranslation servicesRetrievalExpression translationConsumer vocabularySpace constructionTaskInformation
2021
RHybridFinder: An R package to process immunopeptidomic data for putative hybrid peptide discovery
Saab F, Hamelin D, Ma Q, Kovalchik K, Sirois I, Faridi P, Li C, Purcell A, Kubiniok P, Caron E. RHybridFinder: An R package to process immunopeptidomic data for putative hybrid peptide discovery. STAR Protocols 2021, 2: 100875. PMID: 34746858, PMCID: PMC8551247, DOI: 10.1016/j.xpro.2021.100875.Peer-Reviewed Original Research
2019
Large expert-curated database for benchmarking document similarity detection in biomedical literature search
Brown P, Tan A, El-Esawi M, Liehr T, Blanck O, Gladue D, Almeida G, Cernava T, Sorzano C, Yeung A, Engel M, Chandrasekaran A, Muth T, Staege M, Daulatabad S, Widera D, Zhang J, Meule A, Honjo K, Pourret O, Yin C, Zhang Z, Cascella M, Flegel W, Goodyear C, van Raaij M, Bukowy-Bieryllo Z, Campana L, Kurniawan N, Lalaouna D, Hüttner F, Ammerman B, Ehret F, Cobine P, Tan E, Han H, Xia W, McCrum C, Dings R, Marinello F, Nilsson H, Nixon B, Voskarides K, Yang L, Costa V, Bengtsson-Palme J, Bradshaw W, Grimm D, Kumar N, Martis E, Prieto D, Sabnis S, Amer S, Liew A, Perco P, Rahimi F, Riva G, Zhang C, Devkota H, Ogami K, Basharat Z, Fierz W, Siebers R, Tan K, Boehme K, Brenneisen P, Brown J, Dalrymple B, Harvey D, Ng G, Werten S, Bleackley M, Dai Z, Dhariwal R, Gelfer Y, Hartmann M, Miotla P, Tamaian R, Govender P, Gurney-Champion O, Kauppila J, Zhang X, Echeverría N, Subhash S, Sallmon H, Tofani M, Bae T, Bosch O, Cuív P, Danchin A, Diouf B, Eerola T, Evangelou E, Filipp F, Klump H, Kurgan L, Smith S, Terrier O, Tuttle N, Ascher D, Janga S, Schulte L, Becker D, Browngardt C, Bush S, Gaullier G, Ide K, Meseko C, Werner G, Zaucha J, Al-Farha A, Greenwald N, Popoola S, Rahman S, Xu J, Yang S, Hiroi N, Alper O, Baker C, Bitzer M, Chacko G, Debrabant B, Dixon R, Forano E, Gilliham M, Kelly S, Klempnauer K, Lidbury B, Lin M, Lynch I, Ma W, Maibach E, Mather D, Nandakumar K, Ohgami R, Parchi P, Tressoldi P, Xue Y, Armitage C, Barraud P, Chatzitheochari S, Coelho L, Diao J, Doxey A, Gobet A, Hu P, Kaiser S, Mitchell K, Salama M, Shabalin I, Song H, Stevanovic D, Yadollahpour A, Zeng E, Zinke K, Alimba C, Beyene T, Cao Z, Chan S, Gatchell M, Kleppe A, Piotrowski M, Torga G, Woldesemayat A, Cosacak M, Haston S, Ross S, Williams R, Wong A, Abramowitz M, Effiong A, Lee S, Abid M, Agarabi C, Alaux C, Albrecht D, Atkins G, Beck C, Bonvin A, Bourke E, Brand T, Braun R, Bull J, Cardoso P, Carter D, Delahay R, Ducommun B, Duijf P, Epp T, Eskelinen E, Fallah M, Farber D, Fernandez-Triana J, Feyerabend F, Florio T, Friebe M, Furuta S, Gabrielsen M, Gruber J, Grybos M, Han Q, Heinrich M, Helanterä H, Huber M, Jeltsch A, Jiang F, Josse C, Jurman G, Kamiya H, de Keersmaecker K, Kristiansson E, de Leeuw F, Li J, Liang S, Lopez-Escamez J, Lopez-Ruiz F, Marchbank K, Marschalek R, Martín C, Miele A, Montagutelli X, Morcillo E, Nicoletti R, Niehof M, O’Toole R, Ohtomo T, Oster H, Palma J, Paterson R, Peifer M, Portilla M, Portillo M, Pritchard A, Pusch S, Raghava G, Roberts N, Ross K, Schuele B, Sergeant K, Shen J, Stella A, Sukocheva O, Uversky V, Vanneste S, Villet M, Viveiros M, Vorholt J, Weinstock C, Yamato M, Zabetakis I, Zhao X, Ziegler A, Aizat W, Atlas L, Bridges K, Chakraborty S, Deschodt M, Domingues H, Esfahlani S, Falk S, Guisado J, Kane N, Kueberuwa G, Lau C, Liang D, Liu E, Luu A, Ma C, Ma L, Moyer R, Norris A, Panthee S, Parsons J, Peng Y, Pinto I, Reschke C, Sillanpää E, Stewart C, Uhle F, Yang H, Zhou K, Zhu S, Ashry M, Bergsland N, Berthold M, Chen C, Colella V, Cuypers M, Eskew E, Fan X, Gajda M, Gonzálezlez-Prendes R, Goodin A, Graham E, Groen E, Gutiérrez-Sacristán A, Habes M, Heffler E, Higginbottom D, Janzen T, Jayaraman J, Jibb L, Jongen S, Kinyanjui T, Koleva-Kolarova R, Li Z, Liu Y, Lund B, Lussier A, Ma L, Mier P, Moore M, Nagler K, Orme M, Pearson J, Prajapati A, Saito Y, Tröder S, Uchendu F, Verloh N, Voutchkova D, Abu-Zaid A, Bakkach J, Baumert P, Dono M, Hanson J, Herbelet S, Hobbs E, Kulkarni A, Kumar N, Liu S, Loft N, Reddan T, Senghore T, Vindin H, Xu H, Bannon R, Chen B, Cheung J, Cooper J, Esnakula A, Feghali K, Ghelardi E, Gnasso A, Horbar J, Lai H, Li J, Ma L, Ma R, Pan Z, Peres M, Pranata R, Seow E, Sydes M, Testoni I, Westermair A, Yang Y, Afnan M, Albiol J, Albuquerque L, Amiya E, Amorim R, An Q, Andersen S, Aplin J, Argyropoulos C, Asmann Y, Assaeed A, Atanasov A, Atchison D, Avery S, Avillach P, Baade P, Backman L, Badie C, Baldi A, Ball E, Bardot O, Barnett A, Basner M, Batra J, Bazanova O, Beale A, Beddoe T, Bell M, Berezikov E, Berners-Price S, Bernhardt P, Berry E, Bessa T, Billington C, Birch J, Blakely R, Blaskovich M, Blum R, Boelaert M, Bogdanos D, Bosch C, Bourgoin T, Bouvard D, Boykin L, Bradley G, Braun D, Brownlie J, Brühl A, Burt A, Butler L, Byrareddy S, Byrne H, Cabantous S, Calatayud S, Candal E, Carlson K, Casillas S, Castelvetro V, Caswell P, Cavalli G, Cerovsky V, Chagoyen M, Chen C, Chen D, Chen H, Chen H, Chen J, Chen Y, Cheng C, Cheng J, Chinapaw M, Chinopoulos C, Cho W, Chong L, Chowdhury D, Chwalibog A, Ciresi A, Cockcroft S, Conesa A, Cook P, Cooper D, Coqueret O, Corea E, Costa E, Coupland C, Crawford S, Cruz A, Cui H, Cui Q, Culver D, D’Angiulli A, Dahms T, Daigle F, Dalgleish R, Danielsen H, Darras S, Davidson S, Day D, Degirmenci V, Demaison L, Devriendt K, Ding J, Dogan Y, Dong X, Donner C, Dressick W, Drevon C, Duan H, Ducho C, Dumaz N, Dwarakanath B, Ebell M, Eisenhardt S, Elkum N, Engel N, Erickson T, Fairhead M, Faville M, Fejzo M, Festa F, Feteira A, Flood-Page P, Forsayeth J, Fox S, Franks S, Frentiu F, Frilander M, Fu X, Fujita S, Galea I, Galluzzi L, Gani F, Ganpule A, García-Alix A, Gedye K, Giordano M, Giunta C, Gleeson P, Goarant C, Gong H, Gora D, Gough M, Goyal R, Graham K, Grande-Pérez A, Graves P, Greidanus H, Grice D, Grunau C, Gumulya Y, Guo Y, Gurevich V, Gusev O, Hacker E, Hage S, Hagen G, Hahn S, Haller D, Hammerschmidt S, Han J, Han R, Handfield M, Hapuarachchi H, Harder T, Hardingham J, Heck M, Heers M, Hew K, Higuchi Y, St Hilaire C, Hilton R, Hodzic E, Hone A, Hongoh Y, Hu G, Huber H, Hueso L, Huirne J, Hurt L, Idborg H, Ikeo K, Ingley E, Jakeman P, Jensen A, Jia H, Jia H, Jia S, Jiang J, Jiang X, Jin Y, Jo D, Johnson A, Johnston M, Jonscher K, Jorens P, Jorgensen J, Joubert J, Jung S, M A, Kahan T, Kamboj S, Kang Y, Karamanos Y, Karp N, Kelly R, Kenna R, Kennedy J, Kersten B, Khalaf R, Khalid J, Khatlani T, Khider T, Kijanka G, King S, Kluz T, Knox P, Kobayashi T, Koch K, Kohonen-Corish M, Kong X, Konkle-Parker D, Korpela K, Kostrikis L, Kraiczy P, Kratz H, Krause G, Krebsbach P, Kristensen S, Kumari P, Kunimatsu A, Kurdak H, Kwon Y, Lachat C, Lagisz M, Laky B, Lammerding J, Lange M, Larrosa M, Laslett A, LeClair E, Lee K, Lee M, Lee M, Li G, Li J, Lieb K, Lim Y, Lindsey M, Line P, Liu D, Liu F, Liu H, Liu H, Lloyd V, Lo T, Locci E, Loidl J, Lorenzen J, Lorkowski S, Lovell N, Lu H, Lu W, Lu Z, Luengo G, Lundh L, Lysy P, Mabb A, Mack H, Mackey D, Mahdavi S, Maher P, Maher T, Maity S, Malgrange B, Mamoulakis C, Mangoni A, Manke T, Manstead A, Mantalaris A, Marsal J, Marschall H, Martin F, Martinez-Raga J, Martinez-Salas E, Mathieu D, Matsui Y, Maza E, McCutcheon J, McKay G, McMillan B, McMillan N, Meads C, Medina L, Merrick B, Metzger D, Meunier F, Michaelis M, Micheau O, Mihara H, Mintz E, Mizukami T, Moalic Y, Mohapatra D, Monteiro A, Montes M, Moran J, Morozov S, Mort M, Murai N, Murphy D, Murphy S, Murray S, Naganawa S, Nammi S, Nasios G, Natoli R, Nguyen F, Nicol C, van Nieuwerburgh F, Nilsen E, Nobile C, O’Mahony M, Ohlsson S, Olatunbosun O, Olofsson P, Ortiz A, Ostrikov K, Otto S, Outeiro T, Ouyang S, Paganoni S, Page A, Palm C, Paradies Y, Parsons M, Parsons N, Pascal P, Paul E, Peckham M, Pedemonte N, Pellizzon M, Petrelli M, Pichugin A, Pinto C, Plevris J, Pollesello P, Polz M, Ponti G, Porcelli P, Prince M, Quinn G, Quinn T, Ramula S, Rappsilber J, Rehfeldt F, Reiling J, Remacle C, Rezaei M, Riddick E, Ritter U, Roach N, Roberts D, Robles G, Rodrigues T, Rodriguez C, Roislien J, Roobol M, Rowe J, Ruepp A, van Ruitenbeek J, Rust P, Saad S, Sack G, Santos M, Saudemont A, Sava G, Schrading S, Schramm A, Schreiber M, Schuler S, Schymkowitz J, Sczyrba A, Seib K, Shi H, Shimada T, Shin J, Shortt C, Silveyra P, Skinner D, Small I, Smeets P, So P, Solano F, Sonenshine D, Song J, Southall T, Speakman J, Srinivasan M, Stabile L, Stasiak A, Steadman K, Stein N, Stephens A, Stewart D, Stine K, Storlazzi C, Stoynova N, Strzalka W, Suarez O, Sultana T, Sumant A, Summers M, Sun G, Tacon P, Tanaka K, Tang H, Tanino Y, Targett-Adams P, Tayebi M, Tayyem R, Tebbe C, Telfer E, Tempel W, Teodorczyk-Injeyan J, Thijs G, Thorne S, Thrift A, Tiffon C, Tinnefeld P, Tjahjono D, Tolle F, Toth E, del Tredici A, Tsapas A, Tsirigotis K, Turak A, Tzotzos G, Udo E, Utsumi T, Vaidyanathan S, Vaillant M, Valsesia A, Vandenbroucke R, Veiga F, Vendrell M, Vesk P, Vickers P, Victor V, Villemur R, Vohl M, Voolstra C, Vuillemin A, Wakelin S, Waldron L, Walsh L, Wang A, Wang F, Wang Y, Watanabe Y, Weigert A, Wen J, Wham C, White E, Wiener J, Wilharm G, Wilkinson S, Willmann R, Wilson C, Wirth B, Wojan T, Wolff M, Wong B, Wu T, Wuerbel H, Xiao X, Xu D, Xu J, Xu J, Xue B, Yalcin S, Yan H, Yang E, Yang S, Yang W, Ye Y, Ye Z, Yli-Kauhaluoma J, Yoneyama H, Yu Y, Yuan G, Yuh C, Zaccolo M, Zeng C, Zevnik B, Zhang C, Zhang L, Zhang L, Zhang Y, Zhang Y, Zhang Z, Zhang Z, Zhao Y, Zhou M, Zuberbier T, Aanei C, Ahmad R, Al-Lawama M, Alanio A, Allardyce J, Alonso-Caneiro D, Atack J, Baier D, Bansal A, Benezeth Y, Berbesque C, Berrevoet F, Biedermann P, Bijleveld E, Bittner F, Blombach F, van den Bos W, Boudreau S, Bramoweth A, Braubach O, Cai Y, Campbell M, Cao Z, Catry T, Chen X, Cheng S, Chung H, Chávez-Fumagalli M, Conway A, Costa B, Cyr N, Dean L, Denzel M, Dlamini S, Dudley K, Dufies M, Ecke T, Eckweiler D, Eixarch E, El-Adawy H, Emmrich J, Eustace A, Falter-Wagner C, Fuss J, Gao J, Gill M, Gloyn L, Goggs R, Govinden U, Greene G, Greiff V, Grundle D, Grüneberg P, Gumede N, Haore G, Harrison P, Hoenner X, Hojsgaard D, Hori H, Ikonomopoulou M, Jeurissen P, Johnson D, Kabra D, Kamagata K, Karmakar C, Kasian O, Kaye L, Khan M, Kim Y, Kish J, Kobold S, Kohanbash G, Kohls G, Kugler J, Kumar G, Lacy-Colson J, Latif A, Lauschke V, Li B, Lim C, Liu F, Liu X, Lu J, Lu Q, Mahavadi P, Marzocchi U, McGarrigle C, van Meerten T, Min R, Moal I, Molari M, Molleman L, Mondal S, van de Mortel T, Moss W, Moultos O, Mukherjee M, Nakayama K, Narayan E, Navaratnarajah, Neumann P, Nie J, Nie Y, Niemeyer F, Nolan F, Nwaiwu O, Oldenmenger W, Olumayede E, Ou J, Pallebage-Gamarallage M, Pearce S, Pelkonen T, Pelleri M, Pereira J, Pheko M, Pinto K, Piovesan A, Pluess M, Podolsky I, Prescott J, Qi D, Qi X, Raikou V, Ranft A, Rhodes J, Rotge J, Rowe A, Saggar M, Schuon R, Shahid S, Shalchyan V, Shirvalkar P, Shiryayev O, Singh J, Smout M, Soares A, Song C, Srivastava K, Srivastava R, Sun J, Szabo A, Szymanski W, Tai C, Takeuchi H, Tanadini-Lang S, Tang F, Tao W, Theron G, Tian C, Tian Y, Tuttle L, Valenti A, Verlot P, Walker M, Wang J, Welter D, Winslade M, Wu D, Wu Y, Xiao H, Xu B, Xu J, Xu Z, Yang D, Yang M, Yankilevich P, You Y, Yu C, Zhan J, Zhang G, Zhang K, Zhang T, Zhang Y, Zhao G, Zhao J, Zhou X, Zhu Z, Ajani P, Anazodo U, Bagloee S, Bail K, Bar I, Bathelt J, Benkeser D, Bernier M, Blanchard A, Boakye D, Bonatsos V, Boon M, Bouboulis G, Bromfield E, Brown J, Bul K, Burton K, Butkowski E, Carroll G, Chao F, Charrier E, Chen X, Chen Y, Chenguang, Choi J, Christoffersen T, Comel J, Cosse C, Cui Y, van Dessel P, Dhaval, Diodato D, Duffey M, Dutt A, Egea L, El-Said M, Faye M, Fernandez-Fernandez B, Foley K, Founou L, Fu F, Gadelkareem R, Galimov E, Garip G, Gemmill A, Gouil Q, Grey J, Gridneva Z, Grothe M, Grébert T, Guerrero F, Guignard L, Haenssgen M, Hasler D, Holgate J, Huang A, Hulse-Kemp A, Jean-Quartier C, Jeon S, Jia Y, Jutzeler C, Kalatzis P, Karim M, Karsay K, Keitel A, Kempe A, Keown J, Khoo C, Khwaja N, Kievit R, Kosanic A, Koutoukidis D, Kramer P, Kumar D, Kırağ N, Lanza G, Le T, Leem J, Leightley D, Leite A, Lercher L, Li Y, Lim R, Lima L, Lin L, Ling T, Liu Y, Liu Z, Lu Y, Lum F, Luo H, Machhi J, Macleod A, Macwan I, Madala H, Madani N, de Maio N, Makowiecki K, Mallinson D, Margelyte R, Maria C, Markonis Y, Marsili L, Mavoa S, McWilliams L, Megersa M, Mendes C, Menichetti J, Mercieca-Bebber R, Miller J, Minde D, Minges A, Mishra E, Mishra V, Moores C, Morrice N, Moskalensky A, Navarin N, Negera E, Nolet P, Nordberg A, Nordén R, Nowicki J, Olova N, Olszewski P, Onzima R, Pan C, Park C, Park D, Park S, Patil C, Pedro S, Perry S, Peter J, Peterson B, Pezzuolo A, Pozdnyakov I, Qian S, Qin L, Rafe A, Raote I, Raza A, Rebl H, Refai O, Regan T, Richa T, Richardson M, Robinson K, Rossoni L, Rouet R, Safaei S, Schneeberger P, Schwotzer D, Sebastian A, Selinski J, Seltmann S, Sha F, Shalev N, Shang J, Singer J, Singh M, Smith T, Solomon-Moore E, Song L, Soraggi S, Stanley R, Steckhan N, Strobl F, Subissi L, Supriyanto I, Surve C, Suzuki T, Syme C, Sörelius K, Tang Y, Tantawy M, Tennakoon S, Teseo S, Toelzer C, Tomov N, Tovar M, Tran L, Tripathi S, Tuladhar A, Ukubuiwe A, Ung C, Valgepea K, Vatanparast H, Vidal A, Wang F, Wang Q, Watari R, Webster R, Webster R, Wei J, Wibowo D, Wingenbach T, Xavier R, Xiao S, Xiong P, Xu S, Xu S, Yao R, Yao W, Yin Q, Yu Y, Zaitsu M, Zeineb Z, Zhan X, Zhang J, Zhang R, Zhang W, Zhang X, Zheng S, Zhou B, Zhou X, Ahmad H, Akinwumi S, Albery G, Alhowimel A, Ali J, Alshehri M, Alsuhaibani M, Anikin A, Azubuike S, Bach-Mortensen A, Baltiansky L, Bartas M, Belachew K, Bhardwaj V, Binder K, Bland N, Boah M, Bullen B, Calabrò G, Callahan T, Cao B, Chalmers K, Chang W, Che Z, Chen A, Chen H, Chen H, Chen Y, Chen Z, Choi Y, Chowdhury M, Christensen M, Cooke R, Cottini M, Covington N, Cunningham C, Delarocque J, Devos L, Dhar A, Ding K, Dong K, Dong Z, Dreyer N, Ekstrand C, Fardet T, Feleke B, Feurer T, Freitas A, Gao T, Asefa N, Giganti F, Grabowski P, Guerra-Mora J, Guo C, Guo X, Gupta H, He S, Heijne M, Heinemann S, Hogrebe A, Huang Z, Iskander-Rizk S, Iyer L, Jahan Y, James A, Joel E, Joffroy B, Jégousse C, Kambondo G, Karnati P, Kaya C, Ke A, Kelly D, Kickert R, Kidibule P, Kieselmann J, Kim H, Kitazawa T, Lamberts A, Li Y, Liang H, Linn S, Litfin T, Liusuo W, Lygirou V, Mahato A, Mai Z, Major R, Mali S, Mallis P, Mao W, Mao W, Marvin-Dowle K, Mason L, Merideth B, Merino-Plaza M, Merlaen B, Messina R, Mishra A, Muhammad J, Musinguzi C, Nanou A, Naqash A, Nguyen J, Nguyen T, Ni D, Nida, Notcovich S, Ohst B, Ollivier Q, Osses D, Peng X, Plantinga A, Pulia M, Rafiq M, Raman A, Raucher-Chéné D, Rawski R, Ray A, Razak L, Rudolf K, Rusch P, Sadoine M, Schmidt A, Schurr R, Searles S, Sharma S, Sheehan B, Shi C, Shohayeb B, Sommerlad A, Strehlow J, Sun X, Sundar R, Taherzadeh G, Tahir N, Tang J, Testa J, Tian Z, Tingting Q, Verheijen G, Vickstrom C, Wang T, Wang X, Wang Z, Wei P, Wilson A, Wyart, Yassine A, Yousefzadeh A, Zare A, Zeng Z, Zhang C, Zhang H, Zhang L, Zhang T, Zhang W, Zhang Z, Zhou J, Zhu D, Adamo V, Adeyemo A, Aggelidou M, Al-Owaifeer A, Al-Riyami A, Alzghari S, Andersen V, Angus K, Asaduzzaman M, Asady H, Ato D, Bai X, Baines R, Ballantyne M, Ban B, Beck J, Ben-Nafa W, Black E, Blancher A, Blankstein R, Bodagh N, Borges P, Brooks A, Brox-Ponce J, Brunetti A, Canham C, Carninci P, Carvajal R, Chang S, Chao J, Chatterjee P, Chen H, Chen Y, Chhatriwalla A, Chikowe I, Chuang T, Collevatti R, Valera-Cornejo D, Cuenda A, Dao M, Dauga D, Deng Z, Devkota K, Doan L, Elewa Y, Fan D, Faruk M, Feifei S, Ferguson T, Fleres F, Foster E, Foster C, Furer T, Gao Y, Garcia-Rivera E, Gazdar A, George R, Ghosh S, Gianchecchi E, Gleason J, Hackshaw A, Hall A, Hall R, Harper P, Hogg W, Huang G, Hunter K, IJzerman A, Jesus C, Jian G, Lewis J, Kanj S, Kaur H, Kelly S, Kheir F, Kichatova V, Kiyani M, Klein R, Kovesi T, Kraschnewski J, Kumar A, Labutin D, Lazo-Langner A, Leclercq G, Li M, Li Q, Li T, Li Y, Liao W, Liao Z, Lin J, Lizer J, Lobreglio G, Lowies C, Lu C, Majeed H, Martin A, Martinez-Sobrido L, Meresh E, Middelveen M, Mohebbi A, Mota J, Mozaheb Z, Muyaya L, Nandhakumar A, Ng S, Obeidat M, Oh D, Owais M, Pace-Asciak P, Panwar A, Park C, Patterson C, Penagos-Tabaree F, Pianosi P, Pinzi V, Pridans C, Psaroulaki A, Pujala R, Pulido-Arjona L, Qi P, Rahman P, K N, Rassaf T, Refardt J, Ricciardi W, Riess O, Rovas A, Sacks F, Saleh S, Sampson C, Schmutz A, Sepanski R, Sharma N, Singh M, Spearman P, Subramaniapillai M, Swali R, Tan C, Tellechea J, Thomas L, Tong X, Vavvas D, Veys R, Vitriol V, Wang H, Wang J, Wang J, Waugh J, Webb S, Williams B, Workman A, Xiang T, Xie L, Xu J, Xu T, Yang C, Yoon J, Yuan C, Zaritsky A, Zhang Y, Zhao H, Zuckerman H, Lyu R, Pullan W, Zhou Y. Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database 2019, 2019: baz085. PMID: 33326193, PMCID: PMC7291946, DOI: 10.1093/database/baz085.Peer-Reviewed Original ResearchDocument recommendation systemBiomedical literature searchGold standard benchmarksDocument pairsBaseline methodsDatabase serverRecommender systemsResearch fieldAnnotated dataSeed articlesSearch enginesRelevant documentsSearch techniqueLiterature search techniquesAnnotationHybrid methodServerDocumentsDescriptorsBenchmarksMethod
2018
TQuest, A Web-Based Platform to Enable Precision Medicine by Linking a Tumor’s Genetic Defects to Therapeutic Options
Gershkovich P, Platt J, Knopf J, Tasoulis MK, Shi W, Pusztai L, Hatzis C. TQuest, A Web-Based Platform to Enable Precision Medicine by Linking a Tumor’s Genetic Defects to Therapeutic Options. JCO Clinical Cancer Informatics 2018, 2: 1-13. PMID: 30652574, DOI: 10.1200/cci.17.00120.Peer-Reviewed Original ResearchConceptsData acquisition layerFull-text indexAcquisition layerUser interfaceData layersPrototype web applicationWeb-based platformWeb applicationRelevance scoresSearch enginesSource codeSoftware toolsSearch resultsInterventional clinical trialsLabel dataClinical trialsTherapeutic optionsPlatformUS FoodMolecular abnormalitiesMetastatic breast cancerPotential therapeutic optionPotential treatment optionTumor DNA sequencingWeb-based modulesDataMed – an open source discovery index for finding biomedical datasets
Chen X, Gururaj A, Ozyurt B, Liu R, Soysal E, Cohen T, Tiryaki F, Li Y, Zong N, Jiang M, Rogith D, Salimi M, Kim H, Rocca-Serra P, Gonzalez-Beltran A, Farcas C, Johnson T, Margolis R, Alter G, Sansone S, Fore I, Ohno-Machado L, Grethe J, Xu H. DataMed – an open source discovery index for finding biomedical datasets. Journal Of The American Medical Informatics Association 2018, 25: 300-308. PMID: 29346583, PMCID: PMC7378878, DOI: 10.1093/jamia/ocx121.Peer-Reviewed Original ResearchIngestion pipelineBiomedical datasetsSearch enginesBiomedical domainAdvanced natural language processingRelevant datasetsUser-entered queryData discovery systemUnified metadata modelData ingestion pipelinesNatural language processingOpen-source packageRetrieval engineTerminology servicesMetadata modelMetadata informationDiscovery systemData reuseDataMedBenchmark datasetsBiomedical dataData indexAverage precisionLanguage processingSource package
2017
User needs analysis and usability assessment of DataMed – a biomedical data discovery index
Dixit R, Rogith D, Narayana V, Salimi M, Gururaj A, Ohno-Machado L, Xu H, Johnson T. User needs analysis and usability assessment of DataMed – a biomedical data discovery index. Journal Of The American Medical Informatics Association 2017, 25: 337-344. PMID: 29202203, PMCID: PMC7378884, DOI: 10.1093/jamia/ocx134.Peer-Reviewed Original ResearchData discoveryUsability evaluationInformation needsUser interfaceBiomedical dataIterative usability evaluationsInformation retrieval toolsUser interface needsHigh-quality metadataResearchers informationCommon search enginesDiscovery systemRetrieval toolsDataMedUser studyRelevance judgmentsSearch enginesUser needsDataset explorationUsability assessmentRetrieval techniquesNew retrieval techniqueIncomplete metadataMetadataUsersSearch Datasets in Literature: A Case Study of GWAS.
Dong X, Zhang Y, Xu H. Search Datasets in Literature: A Case Study of GWAS. AMIA Joint Summits On Translational Science Proceedings 2017, 2017: 40-49. PMID: 28815103, PMCID: PMC5543360.Peer-Reviewed Original ResearchRecognition systemMEDLINE abstractsDataset search enginePattern-based rulesText mining methodsData setsUnderlying data setSearch datasetsData discoverabilityUse casesSearch enginesDataset attributesMining methodsF-measureDomain dictionaryScalable approachHybrid approachDatasetFinderRetrieving literatureDiscoverabilityUltimate goalCase studySetScientific publicationsDATS, the data tag suite to enable discoverability of datasets
Sansone S, Gonzalez-Beltran A, Rocca-Serra P, Alter G, Grethe J, Xu H, Fore I, Lyle J, Gururaj A, Chen X, Kim H, Zong N, Li Y, Liu R, Ozyurt I, Ohno-Machado L. DATS, the data tag suite to enable discoverability of datasets. Scientific Data 2017, 4: 170059. PMID: 28585923, PMCID: PMC5460592, DOI: 10.1038/sdata.2017.59.Peer-Reviewed Original ResearchFinding useful data across multiple biomedical data repositories using DataMed
Ohno-Machado L, Sansone S, Alter G, Fore I, Grethe J, Xu H, Gonzalez-Beltran A, Rocca-Serra P, Gururaj A, Bell E, Soysal E, Zong N, Kim H. Finding useful data across multiple biomedical data repositories using DataMed. Nature Genetics 2017, 49: 816-819. PMID: 28546571, PMCID: PMC6460922, DOI: 10.1038/ng.3864.Peer-Reviewed Original ResearchConceptsBiomedical data repositoriesHealth big dataData setsKnowledge discoveryBig dataMultiple repositoriesSearch enginesData indexFAIR principlesDataMedData repositoryService providersKnowledge initiativesKnowledge expertsBiomedical research communityResearch communityRepositoryScience landscapeUseful dataInteroperabilityMetadataFindabilitySetEngineData
2015
Accuracy of information about the intrauterine device on the Internet
Madden T, Cortez S, Kuzemchak M, Kaphingst K, Politi M. Accuracy of information about the intrauterine device on the Internet. American Journal Of Obstetrics And Gynecology 2015, 214: 499.e1-499.e6. PMID: 26546848, PMCID: PMC4808607, DOI: 10.1016/j.ajog.2015.10.928.Peer-Reviewed Original ResearchConceptsWeb sitesQuality of informationCommon search enginesMost Web sitesWorld Wide Web sitesSearch enginesInternetQuarter of sitesOutdated informationInternet resourcesAccuracy of informationSafety of IUDsOnline sourcesInaccurate informationOnline searchHealth informationInformationAccurate informationSearchEffective methodInconsistent qualityDevicesEngineQualityAccuracy
2012
A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework
Bandrowski A, Cachat J, Li Y, Müller H, Sternberg P, Ciccarese P, Clark T, Marenco L, Wang R, Astakhov V, Grethe J, Martone M. A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework. Database 2012, 2012: bas005. PMID: 22434839, PMCID: PMC3308161, DOI: 10.1093/database/bas005.Peer-Reviewed Original ResearchConceptsNeuroscience Information FrameworkSearch engine systemInformation frameworkManual curation effortsNumber of resourcesAutomated annotation toolWeb servicesResource discoveryDynamic contentConfiguration filesValuable analyticsSearch enginesSoftware toolsCuration pipelineAnnotation toolCuration processInformation resourcesCuration effortsResource ownersHybrid humanNeuroscience dataAddress accessibilityLarger scientific communityManual curationDisplay data
2001
Health Information on the Internet: Accessibility, Quality, and Readability in English and Spanish
Berland GK, Elliott MN, Morales LS, Algazy JI, Kravitz RL, Broder MS, Kanouse DE, Muñoz JA, Puyol JA, Lara M, Watkins KE, Yang H, McGlynn EA. Health Information on the Internet: Accessibility, Quality, and Readability in English and Spanish. JAMA 2001, 285: 2612-2621. PMID: 11368735, PMCID: PMC4182102, DOI: 10.1001/jama.285.20.2612.Peer-Reviewed Original ResearchConceptsSearch enginesWeb sitesRelevant contentHealth informationSimple search termsFirst pageHealth Web sitesWeb-based health informationKey clinical elementsHealth-related informationInternetGraph methodProportion of linksEngineKey informationInformationClinical elementsImplicit reviewAccessibility studiesAccuracyHigher reading levelStructured implicit reviewPagesSearch experimentsAccessibility
2000
PathMaster
Mattie M, Staib L, Stratmann E, Tagare H, Duncan J, Miller P. PathMaster. Journal Of The American Medical Informatics Association 2000, 7: 404-415. PMID: 10887168, PMCID: PMC61444, DOI: 10.1136/jamia.2000.0070404.Peer-Reviewed Original ResearchConceptsDigital image databaseText-based descriptionsFeature extraction routineImage databaseIndexing methodSearch enginesFeature extractionCytopathology imagesCross-reference analysisExtraction routinesImagesPrognostic processInformation contentDescriptorsIndividual cell characteristicsDatabaseCell descriptorsRoutinesRecognition trialsEngineIndex dataExtractionMethodDescription
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply