{"id":"https://openalex.org/W7213635365","doi":"https://doi.org/10.37044/osf.io/7egfm_v1","title":"DBCLS BioHackathon 2026 report: QPX: Pathway analysis environment for non-model organisms","display_name":"DBCLS BioHackathon 2026 report: QPX: Pathway analysis environment for non-model organisms","publication_year":2026,"publication_date":"2026-09-19","ids":{"openalex":"https://openalex.org/W7213635365","doi":"https://doi.org/10.37044/osf.io/7egfm_v1"},"language":"en","primary_location":{"id":"doi:10.37044/osf.io/7egfm_v1","doi":"https://doi.org/10.37044/osf.io/7egfm_v1","is_oa":true,"landing_page_url":"https://doi.org/10.37044/osf.io/7egfm_v1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.37044/osf.io/7egfm_v1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079934306","display_name":"Hidemasa U. Bono","orcid":"https://orcid.org/0000-0003-4413-0651","observed_orcids":["https://orcid.org/0000-0003-4413-0651"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hidemasa Bono","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-4413-0651","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029050658","display_name":"Naoya Oec","orcid":"https://orcid.org/0000-0002-7491-4994","observed_orcids":["https://orcid.org/0000-0002-7491-4994"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Naoya Oec","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-7491-4994","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5152248213","display_name":"Haruka Tanimoto","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Haruka Tanimoto","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5152168624","display_name":"Tomohiro Taguchi","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tomohiro Taguchi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5152198812","display_name":"Amane Kurata","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Amane Kurata","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5034934487","display_name":"Ryo Nozu","orcid":"https://orcid.org/0000-0002-1099-3152","observed_orcids":["https://orcid.org/0000-0002-1099-3152"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ryo Nozu","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-1099-3152","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994999766349792,"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":0.9994999766349792,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0003000000142492354,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pathway-analysis","display_name":"pathway analysis","score":0.734000027179718},{"id":"https://openalex.org/keywords/non-model-organisms","display_name":"non-model organisms","score":0.9919999837875366},{"id":"https://openalex.org/keywords/wikipathways","display_name":"WikiPathways","score":0.8009999990463257},{"id":"https://openalex.org/keywords/ortholog-mapping","display_name":"ortholog mapping","score":0.9760000109672546},{"id":"https://openalex.org/keywords/mitochondrial-complex-i","display_name":"mitochondrial complex I","score":0.7440000176429749},{"id":"https://openalex.org/keywords/arabidopsis","display_name":"Arabidopsis","score":0.8489999771118164},{"id":"https://openalex.org/keywords/rice","display_name":"rice","score":0.9100000262260437},{"id":"https://openalex.org/keywords/hypoxic-stress-response","display_name":"hypoxic stress response","score":0.8989999890327454},{"id":"https://openalex.org/keywords/transcriptome","display_name":"transcriptome","score":0.6579999923706055},{"id":"https://openalex.org/keywords/proteome","display_name":"proteome","score":0.9160000085830688},{"id":"https://openalex.org/keywords/metabolome","display_name":"metabolome","score":0.8980000019073486},{"id":"https://openalex.org/keywords/pathway-maps","display_name":"pathway maps","score":0.5740000009536743},{"id":"https://openalex.org/keywords/pubtator","display_name":"PubTator","score":0.656000018119812}],"concepts":[{"id":"https://openalex.org/C2779230013","wikidata":"https://www.wikidata.org/wiki/Q25303877","display_name":"Pathway analysis","level":4,"score":0.6880999803543091},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6287999749183655},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.5540000200271606},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.5145999789237976},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.48590001463890076},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4713999927043915},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.4593999981880188},{"id":"https://openalex.org/C9927688","wikidata":"https://www.wikidata.org/wiki/Q4915012","display_name":"Biological pathway","level":4,"score":0.438400000333786},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.36500000953674316},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.36340001225471497},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.3573000133037567},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.3230000138282776},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.31470000743865967},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3131999969482422},{"id":"https://openalex.org/C3018449070","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signalling pathways","level":3,"score":0.2768999934196472},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.27619999647140503},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.27379998564720154},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.2709999978542328},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.26930001378059387},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.2685999870300293},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.26350000500679016},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2612000107765198},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.2567000091075897}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.37044/osf.io/7egfm_v1","doi":"https://doi.org/10.37044/osf.io/7egfm_v1","is_oa":true,"landing_page_url":"https://doi.org/10.37044/osf.io/7egfm_v1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},{"id":"pmh:oai:share.osf.io:8e8f4c3d-b3cc-4dfa-8030-8f6907804342","doi":null,"is_oa":true,"landing_page_url":"https://osf.io/7egfm","pdf_url":null,"source":{"id":"https://openalex.org/S4306402587","display_name":"BioHackrXiv (OSF Preprints)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2799848540","host_organization_name":"Center for Open Science","host_organization_lineage":["https://openalex.org/I2799848540"],"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":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.37044/osf.io/7egfm_v1","doi":"https://doi.org/10.37044/osf.io/7egfm_v1","is_oa":true,"landing_page_url":"https://doi.org/10.37044/osf.io/7egfm_v1","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W7118942283","https://openalex.org/W4384039144","https://openalex.org/W4388205473","https://openalex.org/W1986365650","https://openalex.org/W2979585142","https://openalex.org/W7098226090","https://openalex.org/W3026082741","https://openalex.org/W2808852567","https://openalex.org/W2162473677","https://openalex.org/W4402721624"],"abstract_inverted_index":{"We":[0,52],"report":[1],"progress":[2],"on":[3,25],"Quest":[4],"for":[5,14,63,70,87],"Pathways":[6],"with":[7],"eXpression":[8],"(QPX),":[9],"a":[10,32,96],"pathway":[11,56,113],"analysis":[12],"environment":[13],"non-model":[15,72],"organisms,":[16],"developed":[17],"during":[18],"the":[19,71],"DBCLS":[20],"BioHackathon":[21],"2026":[22],"(BH26).":[23],"Building":[24],"prior":[26],"BH23/BH25":[27],"work,":[28],"we":[29],"demonstrated":[30],"PathLift,":[31],"tool":[33],"that":[34],"lifts":[35],"WikiPathways":[36],"GPML":[37],"pathways":[38],"to":[39,91],"other":[40],"species":[41],"via":[42],"ortholog":[43],"mapping,":[44],"using":[45],"an":[46,78],"Arabidopsis-to-rice":[47],"mitochondrial":[48],"complex":[49],"I":[50],"example.":[51],"also":[53],"created":[54],"annotated":[55],"maps":[57,90],"in":[58,100],"QPX":[59,89],"integrating":[60],"transcriptome/proteome":[61],"data":[62,69],"hypoxic":[64],"stress":[65],"response,":[66],"and":[67,94,115],"transcriptome/metabolome":[68],"organism":[73],"Symplocarpus":[74],"renifolius,":[75],"which":[76],"lacks":[77],"established":[79],"gene":[80],"ID":[81,110],"system.":[82],"This":[83],"clarified":[84],"data-formatting":[85],"requirements":[86],"linking":[88],"expression":[92],"tables":[93],"surfaced":[95],"string-identifier":[97],"handling":[98],"issue":[99],"QPX's":[101],"backend,":[102],"reported":[103],"upstream.":[104],"Future":[105],"work":[106],"includes":[107],"reproducible":[108],"ChEBI":[109],"assignment,":[111],"automated":[112],"digitization,":[114],"compound-centered":[116],"functional":[117],"networks":[118],"from":[119],"PubChem/PubTator3":[120],"data.":[121]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-09-20T00:00:00"}
