{"id":"https://openalex.org/W2894180658","doi":"https://doi.org/10.7287/peerj.preprints.27161v1","title":"A look back at the quality of Protein Function Prediction tools in CAFA","display_name":"A look back at the quality of Protein Function Prediction tools in CAFA","publication_year":2018,"publication_date":"2018-08-29","ids":{"openalex":"https://openalex.org/W2894180658","doi":"https://doi.org/10.7287/peerj.preprints.27161v1","mag":"2894180658"},"language":"en","primary_location":{"id":"doi:10.7287/peerj.preprints.27161v1","is_oa":true,"landing_page_url":"https://doi.org/10.7287/peerj.preprints.27161v1","pdf_url":"https://peerj.com/preprints/27161.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://peerj.com/preprints/27161.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032899160","display_name":"Morteza Pourreza Shahri","orcid":"https://orcid.org/0000-0002-2437-9153"},"institutions":[{"id":"https://openalex.org/I23732399","display_name":"Montana State University","ror":"https://ror.org/02w0trx84","country_code":"US","type":"education","lineage":["https://openalex.org/I23732399","https://openalex.org/I4210126032"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Morteza Pourreza Shahri","raw_affiliation_strings":["Gianforte School of Computing, Montana State University, Bozeman, United States"],"affiliations":[{"raw_affiliation_string":"Gianforte School of Computing, Montana State University, Bozeman, United States","institution_ids":["https://openalex.org/I23732399"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050103951","display_name":"Madhusudan Srinivasan","orcid":"https://orcid.org/0000-0003-2228-1934"},"institutions":[{"id":"https://openalex.org/I23732399","display_name":"Montana State University","ror":"https://ror.org/02w0trx84","country_code":"US","type":"education","lineage":["https://openalex.org/I23732399","https://openalex.org/I4210126032"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Madhusudan Srinivasan","raw_affiliation_strings":["Gianforte School of Computing, Montana State University, Bozeman, United States"],"affiliations":[{"raw_affiliation_string":"Gianforte School of Computing, Montana State University, Bozeman, United States","institution_ids":["https://openalex.org/I23732399"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030865383","display_name":"Diane Bimczok","orcid":"https://orcid.org/0000-0002-8817-7243"},"institutions":[{"id":"https://openalex.org/I23732399","display_name":"Montana State University","ror":"https://ror.org/02w0trx84","country_code":"US","type":"education","lineage":["https://openalex.org/I23732399","https://openalex.org/I4210126032"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Diane Bimczok","raw_affiliation_strings":["Department of Microbiology and Immunology, Montana State University, Bozeman, United States"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Immunology, Montana State University, Bozeman, United States","institution_ids":["https://openalex.org/I23732399"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083120673","display_name":"Upulee Kanewala","orcid":"https://orcid.org/0000-0002-5954-1616"},"institutions":[{"id":"https://openalex.org/I23732399","display_name":"Montana State University","ror":"https://ror.org/02w0trx84","country_code":"US","type":"education","lineage":["https://openalex.org/I23732399","https://openalex.org/I4210126032"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Upulee Kanewala","raw_affiliation_strings":["Gianforte School of Computing, Montana State University, Bozeman, United States"],"affiliations":[{"raw_affiliation_string":"Gianforte School of Computing, Montana State University, Bozeman, United States","institution_ids":["https://openalex.org/I23732399"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010719226","display_name":"Indika Kahanda","orcid":"https://orcid.org/0000-0002-4536-6917"},"institutions":[{"id":"https://openalex.org/I23732399","display_name":"Montana State University","ror":"https://ror.org/02w0trx84","country_code":"US","type":"education","lineage":["https://openalex.org/I23732399","https://openalex.org/I4210126032"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Indika Kahanda","raw_affiliation_strings":["Gianforte School of Computing, Montana State University, Bozeman, United States"],"affiliations":[{"raw_affiliation_string":"Gianforte School of Computing, Montana State University, Bozeman, United States","institution_ids":["https://openalex.org/I23732399"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5032899160"],"corresponding_institution_ids":["https://openalex.org/I23732399"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.12969959,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10260","display_name":"Software Engineering Research","score":0.9936000108718872,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10260","display_name":"Software Engineering Research","score":0.9936000108718872,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9697999954223633,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9603999853134155,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/oracle","display_name":"Oracle","score":0.7968769073486328},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7337300777435303},{"id":"https://openalex.org/keywords/test","display_name":"Test (biology)","score":0.6101023554801941},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5981322526931763},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5549505352973938},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5097036361694336},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.48088935017585754},{"id":"https://openalex.org/keywords/test-set","display_name":"Test set","score":0.46760669350624084},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.4574609696865082},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4529607892036438},{"id":"https://openalex.org/keywords/quality-assurance","display_name":"Quality assurance","score":0.4163249731063843},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3582598567008972},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3350745439529419},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.31813710927963257},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2967444062232971},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08576399087905884},{"id":"https://openalex.org/keywords/operations-management","display_name":"Operations management","score":0.06304046511650085}],"concepts":[{"id":"https://openalex.org/C55166926","wikidata":"https://www.wikidata.org/wiki/Q2892946","display_name":"Oracle","level":2,"score":0.7968769073486328},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7337300777435303},{"id":"https://openalex.org/C2777267654","wikidata":"https://www.wikidata.org/wiki/Q3519023","display_name":"Test (biology)","level":2,"score":0.6101023554801941},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5981322526931763},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5549505352973938},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5097036361694336},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.48088935017585754},{"id":"https://openalex.org/C169903167","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Test set","level":2,"score":0.46760669350624084},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.4574609696865082},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4529607892036438},{"id":"https://openalex.org/C106436119","wikidata":"https://www.wikidata.org/wiki/Q836575","display_name":"Quality assurance","level":3,"score":0.4163249731063843},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3582598567008972},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3350745439529419},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.31813710927963257},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2967444062232971},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08576399087905884},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.06304046511650085},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C2778618615","wikidata":"https://www.wikidata.org/wiki/Q4008393","display_name":"External quality assessment","level":2,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.7287/peerj.preprints.27161v1","is_oa":true,"landing_page_url":"https://doi.org/10.7287/peerj.preprints.27161v1","pdf_url":"https://peerj.com/preprints/27161.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.7287/peerj.preprints.27161v1","is_oa":true,"landing_page_url":"https://doi.org/10.7287/peerj.preprints.27161v1","pdf_url":"https://peerj.com/preprints/27161.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2894180658.pdf","grobid_xml":"https://content.openalex.org/works/W2894180658.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2073713056","https://openalex.org/W2625833328","https://openalex.org/W1533177136","https://openalex.org/W3110702597"],"abstract_inverted_index":{"The":[0,23,46],"Critical":[1],"Assessment":[2],"of":[3,34,60,69,154],"protein":[4],"Function":[5],"Annotation":[6],"algorithms":[7],"(CAFA)":[8],"is":[9,57,96],"a":[10,61,70,97,116,131,152],"large-scale":[11],"experiment":[12],"for":[13,18,82],"assessing":[14],"the":[15,58,74,83,90,105,125,136,161,175,183],"computational":[16],"models":[17,24],"automated":[19],"function":[20],"prediction":[21,35],"(AFP).":[22],"presented":[25],"in":[26,32],"CAFA":[27],"have":[28],"shown":[29],"excellent":[30],"promise":[31],"terms":[33],"accuracy,":[36],"but":[37],"quality":[38],"assurance":[39],"has":[40,118],"been":[41],"paid":[42],"relatively":[43],"less":[44],"attention.":[45],"main":[47],"challenge":[48],"associated":[49],"with":[50],"conducting":[51],"systematic":[52],"testing":[53,94],"on":[54,186],"AFP":[55,84,87,148],"software":[56],"lack":[59],"test":[62,71,101,117,145,176,184],"oracle,":[63],"which":[64],"determines":[65,114],"passing":[66],"or":[67,120],"failing":[68],"case;":[72],"unfortunately,":[73],"exact":[75],"expected":[76],"outcomes":[77],"are":[78],"not":[79],"well":[80],"defined":[81],"task.":[85],"Thus,":[86],"tools":[88,149,172,180],"face":[89,104],"oracle":[91,106],"problem.":[92],"Metamorphic":[93],"(MT)":[95],"technique":[98],"used":[99],"to":[100,130,135,144,164],"programs":[102],"that":[103,156,170],"problem":[107],"using":[108],"metamorphic":[109],"relations":[110],"(MRs).":[111],"A":[112],"MR":[113],"whether":[115],"passed":[119],"failed":[121],"by":[122,150],"specifying":[123],"how":[124],"output":[126],"should":[127],"change":[128,133],"according":[129],"specific":[132],"made":[134],"input.":[137],"In":[138],"this":[139],"work,":[140],"we":[141,168],"use":[142],"MT":[143],"nine":[146],"CAFA2":[147],"defining":[151],"set":[153],"MRs":[155],"apply":[157],"input":[158],"transformations":[159],"at":[160],"protein-level.":[162],"According":[163],"our":[165],"initial":[166],"testing,":[167],"observe":[169],"several":[171],"fail":[173],"all":[174,182],"cases":[177,185],"and":[178],"two":[179],"pass":[181],"different":[187],"GO":[188],"ontologies.":[189]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
