{"id":"https://openalex.org/W1973110501","doi":"https://doi.org/10.1186/1751-0473-4-2","title":"GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction","display_name":"GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction","publication_year":2009,"publication_date":"2009-01-26","ids":{"openalex":"https://openalex.org/W1973110501","doi":"https://doi.org/10.1186/1751-0473-4-2","mag":"1973110501","pmid":"https://pubmed.ncbi.nlm.nih.gov/19171033"},"language":"en","primary_location":{"id":"doi:10.1186/1751-0473-4-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-4-2","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-4-2","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-4-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024303177","display_name":"Fiona Browne","orcid":"https://orcid.org/0000-0003-0443-4730"},"institutions":[{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Fiona Browne","raw_affiliation_strings":["School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK. hy.wang@ulster.ac.uk","School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK. hy.wang@ulster.ac.uk","institution_ids":["https://openalex.org/I138801177"]},{"raw_affiliation_string":"School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK#TAB#","institution_ids":["https://openalex.org/I138801177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100379058","display_name":"Haiying Wang","orcid":"https://orcid.org/0000-0001-8358-9065"},"institutions":[{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Haiying Wang","raw_affiliation_strings":["School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK","School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK","institution_ids":["https://openalex.org/I138801177"]},{"raw_affiliation_string":"School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK#TAB#","institution_ids":["https://openalex.org/I138801177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024401909","display_name":"Huiru Zheng","orcid":"https://orcid.org/0000-0001-7648-8709"},"institutions":[{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Huiru Zheng","raw_affiliation_strings":["School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK","School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK","institution_ids":["https://openalex.org/I138801177"]},{"raw_affiliation_string":"School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK#TAB#","institution_ids":["https://openalex.org/I138801177"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050612781","display_name":"Francisco Azuaje","orcid":"https://orcid.org/0000-0002-9207-9072"},"institutions":[{"id":"https://openalex.org/I4405259354","display_name":"Centre de Recherche Public de la Sant\u00e9","ror":"https://ror.org/02485re30","country_code":"LU","type":"nonprofit","lineage":["https://openalex.org/I4405259354"]}],"countries":["LU"],"is_corresponding":false,"raw_author_name":"Francisco Azuaje","raw_affiliation_strings":["Laboratory of Cardiovascular Research, Research Centre for Public Health (CRP-Sant\u00e9), 1A rue Thomas Edison, Strassen, L-1445, Luxembourg","Laboratory of Cardiovascular Research, Research Centre for Public Health (CRP-Sant\u00e9), Strassen, Luxembourg"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Cardiovascular Research, Research Centre for Public Health (CRP-Sant\u00e9), 1A rue Thomas Edison, Strassen, L-1445, Luxembourg","institution_ids":["https://openalex.org/I4405259354"]},{"raw_affiliation_string":"Laboratory of Cardiovascular Research, Research Centre for Public Health (CRP-Sant\u00e9), Strassen, Luxembourg","institution_ids":["https://openalex.org/I4405259354"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100379058"],"corresponding_institution_ids":["https://openalex.org/I138801177"],"apc_list":{"value":2040,"currency":"USD","value_usd":2040},"apc_paid":{"value":2040,"currency":"USD","value_usd":2040},"fwci":1.1332,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.75557819,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"4","issue":"1","first_page":"2","last_page":"2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9067999720573425,"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"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9067999720573425,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.015699999406933784,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T13127","display_name":"Biotin and Related Studies","score":0.011900000274181366,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7883962392807007},{"id":"https://openalex.org/keywords/upload","display_name":"Upload","score":0.6001803278923035},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.5894572138786316},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.5553292632102966},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5348716378211975},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4942610263824463},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.48746752738952637},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.40192711353302},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.36475062370300293},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3385792672634125},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32711705565452576},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.11244693398475647},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08854135870933533}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7883962392807007},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.6001803278923035},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.5894572138786316},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.5553292632102966},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5348716378211975},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4942610263824463},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.48746752738952637},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40192711353302},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.36475062370300293},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3385792672634125},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32711705565452576},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.11244693398475647},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08854135870933533},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1751-0473-4-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-4-2","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-4-2","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},{"id":"pmid:19171033","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19171033","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source code for biology and medicine","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2636808","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2636808","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Source Code Biol Med","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1751-0473-4-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-4-2","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-4-2","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1973110501.pdf","grobid_xml":"https://content.openalex.org/works/W1973110501.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1842747800","https://openalex.org/W1986071441","https://openalex.org/W2027918926","https://openalex.org/W2043568498","https://openalex.org/W2088216962","https://openalex.org/W2101674614","https://openalex.org/W2103017472","https://openalex.org/W2116447934","https://openalex.org/W2124354935","https://openalex.org/W2136957665","https://openalex.org/W2149310258","https://openalex.org/W2917431650"],"related_works":["https://openalex.org/W2366107444","https://openalex.org/W2944823289","https://openalex.org/W4388145910","https://openalex.org/W1976205134","https://openalex.org/W3037018281","https://openalex.org/W2381570729","https://openalex.org/W4248336175","https://openalex.org/W2972592048","https://openalex.org/W2358319515","https://openalex.org/W2377717868"],"abstract_inverted_index":{"BACKGROUND:":[0],"Information":[1,75,130],"about":[2],"protein":[3,10,186,200,214],"interaction":[4,150],"networks":[5],"is":[6,108,134,192,208,256],"fundamental":[7],"to":[8,37,66,119,144,184,210,250,258],"understanding":[9],"function":[11],"and":[12,24,47,59,70,79,96,157,168,218,220,242],"cellular":[13,216],"processes.":[14],"Interaction":[15],"patterns":[16],"among":[17],"proteins":[18,56,61,82,183],"can":[19,92,164,181,197,231],"suggest":[20],"new":[21,30],"drug":[22],"targets":[23],"aid":[25],"in":[26,152,203,223],"the":[27,100,142,171],"design":[28],"of":[29,72,89,103,228],"therapeutic":[31],"interventions.":[32],"Efforts":[33],"have":[34],"been":[35],"made":[36],"map":[38],"interactions":[39,222],"on":[40,76,131,213],"a":[41,109,135,161,195,233],"proteomic-wide":[42],"scale":[43],"using":[44],"both":[45,94],"experimental":[46],"computational":[48,68],"techniques.":[49],"Reference":[50,126],"datasets":[51,105,147,230],"that":[52,138],"contain":[53],"known":[54,77],"interacting":[55,78,81],"(positive":[57],"cases)":[58,63],"non-interacting":[60],"(negative":[62],"are":[64,83],"essential":[65],"support":[67],"prediction":[69,151],"validation":[71],"protein-protein":[73,149],"interactions.":[74],"non":[80],"usually":[84],"stored":[85],"within":[86],"databases.":[87],"Extraction":[88],"these":[90],"data":[91],"be":[93,165,232],"complex":[95,187,201],"time":[97,234],"consuming.":[98],"Although,":[99],"automatic":[101],"construction":[102,227],"reference":[104,146,162,229,253],"for":[106,112,148,160,199],"classification":[107],"useful":[110],"resource":[111,116],"researchers":[113,140],"no":[114],"public":[115],"currently":[117],"exists":[118],"perform":[120],"this":[121,245],"task.":[122],"RESULTS:":[123],"GRIP":[124,173,207,240,255],"(Gold":[125],"dataset":[127,163],"constructor":[128],"from":[129],"Protein":[132],"complexes)":[133],"web-based":[136],"system":[137],"provides":[139,175],"with":[141],"functionality":[143],"create":[145],"Saccharomyces":[153,204,224],"cerevisiae.":[154,205,225],"Both":[155],"positive":[156],"negative":[158],"cases":[159],"extracted,":[166],"organised":[167],"downloaded":[169],"by":[170,247],"user.":[172],"also":[174],"an":[176],"upload":[177],"facility":[178,191],"whereby":[179],"users":[180,249],"submit":[182],"determine":[185],"membership.":[188],"A":[189],"search":[190,198],"provided":[193],"where":[194],"user":[196],"information":[202,212],"CONCLUSION:":[206],"developed":[209],"retrieve":[211],"complex,":[215],"localisation,":[217],"physical":[219],"genetic":[221],"Manual":[226],"consuming":[235],"process":[236,246],"requiring":[237],"programming":[238],"knowledge.":[239],"simplifies":[241],"speeds":[243],"up":[244],"allowing":[248],"automatically":[251],"construct":[252],"datasets.":[254],"free":[257],"access":[259],"at":[260],"http://rosalind.infj.ulst.ac.uk/GRIP/.":[261]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
