{"id":"https://openalex.org/W3116802215","doi":"https://doi.org/10.1093/bioinformatics/btaa811","title":"Padhoc: a computational pipeline for pathway reconstruction on the fly","display_name":"Padhoc: a computational pipeline for pathway reconstruction on the fly","publication_year":2020,"publication_date":"2020-09-09","ids":{"openalex":"https://openalex.org/W3116802215","doi":"https://doi.org/10.1093/bioinformatics/btaa811","mag":"3116802215","pmid":"https://pubmed.ncbi.nlm.nih.gov/33381819"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa811","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa811","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/Supplement_2/i795/35336735/btaa811.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/Supplement_2/i795/35336735/btaa811.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048191322","display_name":"Salvador Casan\u00ed-Gald\u00f3n","orcid":"https://orcid.org/0000-0001-8714-3001"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Salvador Casan\u00ed-Gald\u00f3n","raw_affiliation_strings":["Biobam Bioinformatics S.L , Valencia 46005, Spain"],"affiliations":[{"raw_affiliation_string":"Biobam Bioinformatics S.L , Valencia 46005, Spain","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091529220","display_name":"C\u00e9cile Pereira","orcid":"https://orcid.org/0000-0001-8050-3019"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cecile Pereira","raw_affiliation_strings":["EURA NOVA , Marseille 13382, France","Institute for Food and Agricultural Sciences, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32603, USA"],"affiliations":[{"raw_affiliation_string":"EURA NOVA , Marseille 13382, France","institution_ids":[]},{"raw_affiliation_string":"Institute for Food and Agricultural Sciences, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32603, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002377126","display_name":"Ana Conesa","orcid":"https://orcid.org/0000-0001-9597-311X"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ana Conesa","raw_affiliation_strings":["Institute for Food and Agricultural Sciences, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32603, USA"],"affiliations":[{"raw_affiliation_string":"Institute for Food and Agricultural Sciences, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32603, USA","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5002377126"],"corresponding_institution_ids":["https://openalex.org/I33213144"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3314,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.58006413,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"36","issue":"Supplement_2","first_page":"i795","last_page":"i803"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9915000200271606,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9915000200271606,"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/T10895","display_name":"Species Distribution and Climate Change","score":0.9200000166893005,"subfield":{"id":"https://openalex.org/subfields/2302","display_name":"Ecological Modeling"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.8094009160995483},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6655173301696777},{"id":"https://openalex.org/keywords/on-the-fly","display_name":"On the fly","score":0.6232181191444397},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33761781454086304},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.22678494453430176},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13485077023506165},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.10469529032707214}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.8094009160995483},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6655173301696777},{"id":"https://openalex.org/C2781020372","wikidata":"https://www.wikidata.org/wiki/Q533093","display_name":"On the fly","level":2,"score":0.6232181191444397},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33761781454086304},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.22678494453430176},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13485077023506165},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.10469529032707214}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaa811","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa811","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/Supplement_2/i795/35336735/btaa811.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33381819","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33381819","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa811","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa811","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/Supplement_2/i795/35336735/btaa811.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.6700000166893005}],"awards":[{"id":"https://openalex.org/G256786057","display_name":null,"funder_award_id":"2015-70016-23029","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"}],"funders":[{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"},{"id":"https://openalex.org/F4320332299","display_name":"National Institute of Food and Agriculture","ror":"https://ror.org/05qx3fv49"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3116802215.pdf","grobid_xml":"https://content.openalex.org/works/W3116802215.grobid-xml"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W4596803","https://openalex.org/W195536640","https://openalex.org/W570990186","https://openalex.org/W1964911061","https://openalex.org/W1973646872","https://openalex.org/W1977622464","https://openalex.org/W1989277387","https://openalex.org/W2011648399","https://openalex.org/W2018711046","https://openalex.org/W2024124003","https://openalex.org/W2024387432","https://openalex.org/W2040676413","https://openalex.org/W2073604872","https://openalex.org/W2074906123","https://openalex.org/W2082448471","https://openalex.org/W2092031590","https://openalex.org/W2092489937","https://openalex.org/W2101727078","https://openalex.org/W2107839259","https://openalex.org/W2108078368","https://openalex.org/W2116351978","https://openalex.org/W2126276057","https://openalex.org/W2135084125","https://openalex.org/W2137464714","https://openalex.org/W2138676914","https://openalex.org/W2142067151","https://openalex.org/W2142638534","https://openalex.org/W2144000913","https://openalex.org/W2144575277","https://openalex.org/W2149369282","https://openalex.org/W2159728029","https://openalex.org/W2160757449","https://openalex.org/W2165253681","https://openalex.org/W2169491861","https://openalex.org/W2247766769","https://openalex.org/W2340716977","https://openalex.org/W2402754383","https://openalex.org/W2537623931","https://openalex.org/W2557833574","https://openalex.org/W2559588208","https://openalex.org/W2591904409","https://openalex.org/W2593008216","https://openalex.org/W2619419337","https://openalex.org/W2732718245","https://openalex.org/W2736196485","https://openalex.org/W2774789440","https://openalex.org/W2787264803","https://openalex.org/W2792322849","https://openalex.org/W2954075147","https://openalex.org/W3013867433","https://openalex.org/W3036534752","https://openalex.org/W4237335579"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W2382290278","https://openalex.org/W4395014643"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
