{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T10:19:19Z","timestamp":1784715559059,"version":"3.55.0"},"reference-count":115,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,8,3]],"date-time":"2023-08-03T00:00:00Z","timestamp":1691020800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Artif. Intell."],"abstract":"<jats:p>While the continuing decline in genotyping and sequencing costs has largely benefited plant research, some key species for meeting the challenges of agriculture remain mostly understudied. As a result, heterogeneous datasets for different traits are available for a significant number of these species. As gene structures and functions are to some extent conserved through evolution, comparative genomics can be used to transfer available knowledge from one species to another. However, such a translational research approach is complex due to the multiplicity of data sources and the non-harmonized description of the data. Here, we provide two pipelines, referred to as structural and functional pipelines, to create a framework for a NoSQL graph-database (Neo4j) to integrate and query heterogeneous data from multiple species. We call this framework Orthology-driven knowledge base framework for translational research (Ortho_KB). The structural pipeline builds bridges across species based on orthology. The functional pipeline integrates biological information, including QTL, and RNA-sequencing datasets, and uses the backbone from the structural pipeline to connect orthologs in the database. Queries can be written using the Neo4j Cypher language and can, for instance, lead to identify genes controlling a common trait across species. To explore the possibilities offered by such a framework, we populated Ortho_KB to obtain OrthoLegKB, an instance dedicated to legumes. The proposed model was evaluated by studying the conservation of a flowering-promoting gene. Through a series of queries, we have demonstrated that our knowledge graph base provides an intuitive and powerful platform to support research and development programmes.<\/jats:p>","DOI":"10.3389\/frai.2023.1191122","type":"journal-article","created":{"date-parts":[[2023,8,3]],"date-time":"2023-08-03T14:27:20Z","timestamp":1691072840000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":9,"title":["Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes"],"prefix":"10.3389","volume":"6","author":[{"given":"Baptiste","family":"Imbert","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan","family":"Kreplak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rapha\u00ebl-Gauthier","family":"Flores","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gr\u00e9goire","family":"Aubert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Judith","family":"Burstin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nadim","family":"Tayeh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,8,3]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.2210.05781","article-title":"Transforming RDF-star to property graphs: A preliminary analysis of transformation approaches \u2013 extended version","author":"Abuoda","year":"2022","journal-title":"arXiv [Preprint]."},{"key":"B2","doi-asserted-by":"publisher","first-page":"13716","DOI":"10.1038\/s41598-021-92680-4","article-title":"Linkage mapping and QTL analysis of flowering time in faba bean","volume":"11","author":"Aguilar-Benitez","year":"2021","journal-title":"Sci. Rep."},{"key":"B3","first-page":"74","volume-title":"Interactive Exploration of Genomic Conservation in Proceedings of Graphics Interface 2020 GI 2020","author":"Bandi","year":"2020"},{"key":"B4","unstructured":"BarrasaJ. Neosemantics (n10s)2022"},{"key":"B5","doi-asserted-by":"publisher","first-page":"474","DOI":"10.1002\/dvg.22877","article-title":"The arabidopsis information resource: making and mining the \u201cgold standard\u201d annotated reference plant genome: tair: making and mining the \u201cgold standard\u201d plant genome","volume":"53","author":"Berardini","year":"2015","journal-title":"Genesis"},{"key":"B6","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1002\/leg3.74","article-title":"The legume information system and associated online genomic resources","volume":"3","author":"Berendzen","year":"2021","journal-title":"Legume Sci."},{"key":"B7","doi-asserted-by":"publisher","first-page":"D344","DOI":"10.1093\/nar\/gkaa977","article-title":"The interpro protein families and domains database: 20 years on","volume":"49","author":"Blum","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"B8","doi-asserted-by":"publisher","first-page":"e101","DOI":"10.1093\/nar\/gkab565","article-title":"TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes","volume":"49","author":"Bucchini","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"B9","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","article-title":"Sensitive protein alignments at tree-of-life scale using DIAMOND","volume":"18","author":"Buchfink","year":"2021","journal-title":"Nat Methods"},{"key":"B10","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"1494","DOI":"10.1093\/pcp\/pcab110","article-title":"MtExpress, a comprehensive and curated RNASEQ-based gene expression atlas for the model legume Medicago truncatula","volume":"62","author":"Carrere","year":"2021","journal-title":"Plant Cell Physiol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1093\/plphys\/kiaa005","article-title":"Genetic regulation of flowering time and inflorescence architecture by MtFDa and MtFTa1 in Medicago truncatula","volume":"185","author":"Cheng","year":"2021","journal-title":"Plant Physiol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"2938","DOI":"10.1093\/bioinformatics\/btx364","article-title":"UpSetR: an R package for the visualization of intersecting sets and their properties","volume":"33","author":"Conway","year":"2017","journal-title":"Bioinf."},{"key":"B14","doi-asserted-by":"publisher","first-page":"D1168","DOI":"10.1093\/nar\/gkx1152","article-title":"The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics","volume":"46","author":"Cooper","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"B15","doi-asserted-by":"publisher","first-page":"D1472","DOI":"10.1093\/nar\/gkaa976","article-title":"LegumeIP V3: from models to crops\u2014an integrative gene discovery platform for translational genomics in legumes","volume":"49","author":"Dai","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.7255559","article-title":"NBISweden\/AGAT: AGAT-v1.0.0","author":"Dainat","year":"2022","journal-title":"Zenodo"},{"key":"B17","doi-asserted-by":"publisher","first-page":"3423","DOI":"10.1093\/bioinformatics\/btr539","article-title":"Pybedtools: a flexible Python library for manipulating genomic datasets and annotations","volume":"27","author":"Dale","year":"2011","journal-title":"Bioinformatics"},{"key":"B18","doi-asserted-by":"publisher","first-page":"2343","DOI":"10.1104\/pp.15.01207","article-title":"Expression pattern similarities support the prediction of orthologs retaining common functions after gene duplication events","volume":"171","author":"Das","year":"2016","journal-title":"Plant Physiol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"gkac1040","DOI":"10.1093\/nar\/gkac1040","article-title":"The proteomexchange consortium at 10 years: 2023 update","volume":"5","author":"Deutsch","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"B20","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"Di Tommaso","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"B21","unstructured":"\u201cLinked data for smart homes: comparing RDF and labeled property graphs,\u201d DonkersA. YangD. BakenN. LDAC2020"},{"key":"B22","doi-asserted-by":"publisher","first-page":"2747","DOI":"10.1093\/molbev\/msaa114","article-title":"Phylogenetic reconstruction based on synteny block and gene adjacencies","volume":"37","author":"Drillon","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.7389537","author":"Dubbelaar","year":"2022","journal-title":"nf-core\/mhcquant: mhcquant 2.4.0 \u2013 Maroon Gold Boxer. Zenodo"},{"key":"B24","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1186\/s13059-015-0721-2","article-title":"OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy","volume":"16","author":"Emms","year":"2015","journal-title":"Genome Biol."},{"key":"B25","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol."},{"key":"B26","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1038\/s41587-020-0439-x","article-title":"The nf-core framework for community-curated bioinformatics pipelines","volume":"38","author":"Ewels","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"B27","unstructured":"Reactome graph database: efficient access to complex pathway datae1005968 FabregatA. KorningerF. ViteriG. SidiropoulosK. Marin-GarciaP. PingP. 10.1371\/journal.pcbi.100596829377902PLoS Comput. Biol.142018"},{"key":"B28","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1186\/s12870-018-1368-4","article-title":"Construction of high-density linkage maps for mapping quantitative trait loci for multiple traits in field pea (Pisum sativum L.)","volume":"18","author":"Gali","year":"2018","journal-title":"BMC Plant Biol."},{"key":"B29","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1016\/j.jare.2021.10.009","article-title":"Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement","volume":"42","author":"Garg","year":"2022","journal-title":"J. Adv. Res."},{"key":"B30","doi-asserted-by":"publisher","first-page":"D1178","DOI":"10.1093\/nar\/gkr944","article-title":"Phytozome: a comparative platform for green plant genomics","volume":"40","author":"Goodstein","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"B31","doi-asserted-by":"publisher","first-page":"D843","DOI":"10.1093\/nar\/gkp798","article-title":"SoyBase, the USDA-ARS soybean genetics and genomics database","volume":"38","author":"Grant","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.7748890","article-title":"RDFLib\/rdflib: RDFlib 6.3.1","author":"Grimnes","year":"2023","journal-title":"Zenodo"},{"key":"B33","doi-asserted-by":"publisher","first-page":"2765","DOI":"10.1074\/mcp.O113.036681","article-title":"The mzTab Data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience","volume":"13","author":"Griss","year":"2014","journal-title":"Mol. Cell. Prot."},{"key":"B34","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1002\/pld3.8","article-title":"CoGe LoadExp+: a web-based suite that integrates next-generation sequencing data analysis workflows and visualization","volume":"1","author":"Grover","year":"2017","journal-title":"Plant Direct"},{"key":"B35","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1186\/s12859-017-1777-7","article-title":"ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding","volume":"18","author":"Guhlin","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"B36","doi-asserted-by":"publisher","first-page":"3416","DOI":"10.1038\/s41598-020-60166-4","article-title":"Evaluation of pulse crops' functional diversity supporting food production","volume":"10","author":"Guiguitant","year":"2020","journal-title":"Sci. Rep."},{"key":"B37","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1002\/tpg2.20121","volume":"10","author":"Ha","year":"2021","journal-title":"A near-complete genome sequence of mungbean (Vigna radiata L.) provides key insights into the modern breeding program. Plant Genome"},{"key":"B38","doi-asserted-by":"crossref","unstructured":"HacklT. AnkenbrandM. Gggenomes: A Grammar of Graphics for Comparative Genomics2023","DOI":"10.32614\/CRAN.package.gggenomes"},{"key":"B39","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1002\/tpg2.20144","article-title":"Genetic basis for lentil adaptation to summer cropping in northern temperate environments","volume":"14","author":"Haile","year":"2021","journal-title":"Plant Genome"},{"key":"B40","unstructured":"HartigO. Reconciliation of RDF2014"},{"key":"B41","doi-asserted-by":"publisher","first-page":"1670","DOI":"10.1111\/pbi.13583","article-title":"KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species","volume":"19","author":"Hassani-Pak","year":"2021","journal-title":"Plant Biotechnol. J."},{"key":"B42","doi-asserted-by":"publisher","first-page":"648","DOI":"10.1104\/pp.107.096818","article-title":"Pea LATE BLOOMER1 Is a GIGANTEA ortholog with roles in photoperiodic flowering, deetiolation, and transcriptional regulation of circadian clock gene homologs","volume":"144","author":"Hecht","year":"2007","journal-title":"Plant Physiol."},{"key":"B43","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1105\/tpc.110.081042","article-title":"The Pea GIGAS gene is a flowering locus t homolog necessary for graft-transmissible specification of flowering but not for responsiveness to photoperiod","volume":"23","author":"Hecht","year":"2011","journal-title":"The Plant Cell"},{"key":"B44","doi-asserted-by":"publisher","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses","volume":"47","author":"Huerta-Cepas","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B45","unstructured":"HumannJ. JungS. ChengC. H. LeeT. ZhengP. FrankM. A resource for pea, lentil, faba bean, and chickpea genetics, genomics and breeding. Proceedings of the International Plant and Animal Genome Conference, 32019"},{"key":"B46","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41586-023-05791-5","article-title":"The giant diploid faba genome unlocks variation in a global protein crop","volume":"26","author":"Jayakodi","year":"2023","journal-title":"Nature"},{"key":"B47","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: genome-scale protein function classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"B48","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1007\/s11032-015-0430-2","article-title":"Orphan crops browser: a bridge between model and orphan crops","volume":"36","author":"Kamei","year":"2016","journal-title":"Mol. Breeding"},{"key":"B49","unstructured":"KansJ. Entrez Direct: E-utilities on the Unix Command Line. National Center for Biotechnology Information (US)2013"},{"key":"B50","doi-asserted-by":"publisher","first-page":"4595","DOI":"10.1007\/s11831-021-09547-0","article-title":"Computational techniques and tools for omics data analysis: state-of-the-art, challenges, and future directions","volume":"28","author":"Kaur","year":"2021","journal-title":"Arch Computat. Methods Eng."},{"key":"B51","unstructured":"\u201cConverting property graphs to RDF: a preliminary study of the practical impact of different mappings,\u201d19 KhayatbashiS. FerradaS. HartigO. 10.1145\/3534540.3534695New York, NYAssociation for Computing MachineryProceedings of the 5th ACM SIGMOD Joint International Workshop on Graph Data Management Experiences & Systems (GRADES) and Network Data Analytics (NDA) GRADES-NDA '222022"},{"key":"B52","doi-asserted-by":"publisher","first-page":"1411","DOI":"10.1038\/s41588-019-0480-1","article-title":"A reference genome for pea provides insight into legume genome evolution","volume":"51","author":"Kreplak","year":"2019","journal-title":"Nat. Genet."},{"key":"B53","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1093\/pcp\/pcu179","article-title":"MTGD: the medicago truncatula genome database","volume":"56","author":"Krishnakumar","year":"2015","journal-title":"Plant Cell Physiol."},{"key":"B54","unstructured":"LaporteM. -A. ValetteL. ArnaudE. CooperL. MeierA. JaiswalP. Comparison of Ontology Mapping Techniques to Map Plant Trait Ontologies. Corvallis, OR: CEUR Workshop Proceedings2016"},{"key":"B55","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1007\/978-3-030-88361-4_29","article-title":"\u201cAgroLD: A knowledge graph for the plant sciences,\u201d","volume-title":"Semantic Web - ISWC 2021 Lecture Notes in Computer Science","author":"Larmande","year":"2021"},{"key":"B56","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1104\/pp.111.180182","article-title":"The Medicago flowering locus T Homolog, MtFTa1, Is a Key Regulator of Flowering Time","volume":"156","author":"Laurie","year":"2011"},{"key":"B57","doi-asserted-by":"publisher","first-page":"D465","DOI":"10.1093\/nar\/gkr1181","article-title":"Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis","volume":"40","author":"Lees","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"B58","doi-asserted-by":"publisher","first-page":"D1221","DOI":"10.1093\/nar\/gkr939","article-title":"LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes","volume":"40","author":"Li","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"B59","doi-asserted-by":"publisher","first-page":"D1189","DOI":"10.1093\/nar\/gkv1237","article-title":"LegumeIP 2.0\u2013a platform for the study of gene function and genome evolution in legumes","volume":"44","author":"Li","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"B60","doi-asserted-by":"publisher","first-page":"3479","DOI":"10.1038\/s41467-022-31112-x","article-title":"The 3D architecture of the pepper genome and its relationship to function and evolution","volume":"13","author":"Liao","year":"2022","journal-title":"Nat. Commun."},{"key":"B61","doi-asserted-by":"publisher","first-page":"3033","DOI":"10.1093\/molbev\/msab098","article-title":"Ten years of collaborative progress in the quest for orthologs","volume":"38","author":"Linard","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"B62","doi-asserted-by":"publisher","first-page":"1250","DOI":"10.1111\/pce.12231","article-title":"Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data: Mercator: sequence functional annotation server","volume":"37","author":"Lohse","year":"2014","journal-title":"Plant Cell Environ."},{"key":"B63","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1111\/j.1365-313X.2007.03326.x","article-title":"How to usefully compare homologous plant genes and chromosomes as DNA sequences","volume":"53","author":"Lyons","year":"2008","journal-title":"The Plant J."},{"key":"B64","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1007\/978-1-60761-175-2_7","article-title":"PANTHER Pathway: an ontology-based pathway database coupled with data analysis tools","volume":"563","author":"Mi","year":"2009","journal-title":"Methods Mol. Biol."},{"key":"B65","doi-asserted-by":"publisher","first-page":"R21","DOI":"10.1530\/JME-18-0055","article-title":"Integrated omics: tools, advances and future approaches","volume":"62","author":"Misra","year":"2019","journal-title":"J. Mol. Endocrinol."},{"key":"B66","doi-asserted-by":"publisher","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: the protein families database in 2021","volume":"49","author":"Mistry","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"B67","doi-asserted-by":"publisher","first-page":"gkz996","DOI":"10.1093\/nar\/gkz996","article-title":"Plant Reactome: a knowledgebase and resource for comparative pathway analysis","volume":"47","author":"Naithani","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B68","unstructured":"SRA Metadata and Submission Overview2023"},{"key":"B69","unstructured":"ArrowsNeo4j Graph Data Platform"},{"key":"B70","unstructured":"The Neo4j Graph Data Platform. Neo4j Graph Data Platform"},{"key":"B71","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1186\/s13007-015-0053-y","article-title":"An ontology approach to comparative phenomics in plants","volume":"11","author":"Oellrich","year":"2015","journal-title":"Plant Methods"},{"key":"B72","doi-asserted-by":"publisher","first-page":"D741","DOI":"10.1093\/nar\/gkj094","article-title":"The rice annotation project database (RAP-DB): hub for Oryza sativa ssp. japonica genome information","volume":"34","author":"Ohyanagi","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"B73","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.7468050","article-title":"nf-core\/fetchngs: nf-core\/fetchngs v1.9 - Plutonium Prancer","author":"Patel","year":"2022","journal-title":"Zenodo"},{"key":"B74","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.7505987","article-title":"nf-core\/rnaseq: nf-core\/rnaseq v3.10.1 \u2013 Plastered Rhodium Rudolph","author":"Patel","year":"2023","journal-title":"Zenodo"},{"key":"B75","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat. Methods"},{"key":"B76","doi-asserted-by":"publisher","first-page":"1017","DOI":"10.1038\/s41477-018-0286-7","article-title":"Whole-genome landscape of Medicago truncatula symbiotic genes","volume":"4","author":"Pecrix","year":"2018","journal-title":"Nature Plants"},{"key":"B77","doi-asserted-by":"publisher","first-page":"giaa100","DOI":"10.1093\/gigascience\/giaa100","article-title":"Construction of a chromosome-scale long-read reference genome assembly for potato","volume":"9","author":"Pham","year":"2020","journal-title":"GigaScience"},{"key":"B78","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"B79","doi-asserted-by":"publisher","DOI":"10.1093\/database\/bay013","article-title":"Micropublication : incentivizing community curation and placing unpublished data into the public domain","author":"Raciti","year":"2018","journal-title":"Database"},{"key":"B80","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1101\/2021.07.23.453237","volume":"24","author":"Ramsay","year":"2021","journal-title":"Genomic rearrangements have consequences for introgression breeding as revealed by genome assemblies of wild and cultivated lentil species. Plant Biol."},{"key":"B81","doi-asserted-by":"publisher","DOI":"10.15454\/TIMQHW","author":"Roussey","year":"2021","journal-title":"BBCH-based Plant Phenological Description Ontology"},{"key":"B82","doi-asserted-by":"publisher","first-page":"782574","DOI":"10.3389\/fpls.2021.782574","article-title":"Legume breeding for the agroecological transition of global agri-food systems: a european perspective","volume":"12","author":"Rubiales","year":"2021","journal-title":"Front. Plant Sci."},{"key":"B83","doi-asserted-by":"publisher","first-page":"965","DOI":"10.3389\/fpls.2019.00965","article-title":"KnowPulse: a web-resource focused on diversity data for pulse crop improvement","volume":"10","author":"Sanderson","year":"2019","journal-title":"Front. Plant Sci."},{"key":"B84","doi-asserted-by":"publisher","first-page":"692","DOI":"10.1038\/s41587-021-01145-6","volume":"40","author":"Santos","year":"2022","journal-title":"A knowledge graph to interpret clinical proteomics data. Nat Biotechnol."},{"key":"B85","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1093\/dnares\/dsn008","article-title":"Genome structure of the legume, lotus japonicus","volume":"15","author":"Sato","year":"2008","journal-title":"DNA Res."},{"key":"B86","doi-asserted-by":"publisher","first-page":"D20","DOI":"10.1093\/nar\/gkab1112","article-title":"Database resources of the national center for biotechnology information","volume":"50","author":"Sayers","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"B87","doi-asserted-by":"publisher","first-page":"879","DOI":"10.1016\/j.molp.2019.01.003","article-title":"MapMan4: a refined protein classification and annotation framework applicable to multi-omics data analysis","volume":"12","author":"Schwacke","year":"2019","journal-title":"Mol. Plant"},{"key":"B88","doi-asserted-by":"publisher","first-page":"100520","DOI":"10.1016\/j.gfs.2021.100520","article-title":"Legumes as a sustainable source of protein in human diets","volume":"28","author":"Semba","year":"2021","journal-title":"Global Food Security"},{"key":"B89","doi-asserted-by":"publisher","first-page":"e0163962","DOI":"10.1371\/journal.pone.0163962","article-title":"SeqKit: a cross-platform and ultrafast toolkit for fastA\/Q file manipulation","volume":"11","author":"Shen","year":"2016","journal-title":"PLoS ONE"},{"key":"B90","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1038\/nature24286","article-title":"DNA sequencing at 40: past, present and future","volume":"550","author":"Shendure","year":"2017","journal-title":"Nature"},{"key":"B91","doi-asserted-by":"publisher","first-page":"326","DOI":"10.3389\/fphys.2012.00326","article-title":"Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice","volume":"3","author":"Shrestha","year":"2012","journal-title":"Front. Physio."},{"key":"B92","doi-asserted-by":"publisher","first-page":"D977","DOI":"10.1093\/nar\/gkac1010","article-title":"The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource","volume":"51","author":"Sollis","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B93","volume-title":"Differential analyses for","author":"Soneson","year":"2016"},{"key":"B94","doi-asserted-by":"publisher","first-page":"e1008260","DOI":"10.1371\/journal.pcbi.1008260","article-title":"Ten simple rules for annotating sequencing experiments","volume":"16","author":"Stevens","year":"2020","journal-title":"PLOS Computat. Biol."},{"key":"B95","doi-asserted-by":"publisher","first-page":"898","DOI":"10.1186\/s12864-021-08212-x","article-title":"A high-continuity and annotated tomato reference genome","volume":"22","author":"Su","year":"2021","journal-title":"BMC Genomics"},{"key":"B96","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1126\/science.1153917","article-title":"Synteny and collinearity in plant genomes","volume":"320","author":"Tang","year":"2008","journal-title":"Science"},{"key":"B97","doi-asserted-by":"publisher","first-page":"D1452","DOI":"10.1093\/nar\/gkaa979","article-title":"Gramene 2021: harnessing the power of comparative genomics and pathways for plant research","volume":"49","author":"Tello-Ruiz","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"B98","doi-asserted-by":"publisher","first-page":"217","DOI":"10.12705\/622.8","article-title":"Legume phylogeny and classification in the 21st century: progress, prospects and lessons for other species\u2013rich clades","volume":"62","author":"Bruneau","year":"2013","journal-title":"TAXON"},{"key":"B99","doi-asserted-by":"publisher","first-page":"e6626","DOI":"10.7717\/peerj.6626","article-title":"The transcriptomic response to a short day to long day shift in leaves of the reference legume Medicago truncatula","volume":"7","author":"Thomson","year":"2019","journal-title":"PeerJ"},{"key":"B100","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1104\/pp.111.189514","article-title":"Dissecting plant genomes with the plaza comparative genomics platform","volume":"158","author":"Van Bel","year":"2012","journal-title":"Plant Physiol."},{"key":"B101","doi-asserted-by":"publisher","first-page":"D1468","DOI":"10.1093\/nar\/gkab1024","article-title":"PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants","volume":"50","author":"Van Bel","year":"2022","journal-title":"Nucleic Acid. Res."},{"key":"B102","doi-asserted-by":"publisher","first-page":"e0198270","DOI":"10.1371\/journal.pone.0198270","article-title":"Agronomic Linked Data (AgroLD): a knowledge-based system to enable integrative biology in agronomy","volume":"13","author":"Venkatesan","year":"2018","journal-title":"PLoS ONE"},{"key":"B103","unstructured":"\u201cA comparison of a graph database and a relational database: a data provenance perspective,\u201d VicknairC. MaciasM. ZhaoZ. NanX. ChenY. WilkinsD. 10.1145\/1900008.1900067Oxford, MSACM PressProceedings of the 48th Annual Southeast Regional Conference on - ACM SE '102010"},{"key":"B104","doi-asserted-by":"publisher","first-page":"1221","DOI":"10.1093\/gbe\/evy081","article-title":"Comparative genomics reveals thousands of novel chemosensory genes and massive changes in chemoreceptor repertories across chelicerates","volume":"10","author":"Vizueta","year":"2018","journal-title":"Genome Biol. Evol."},{"key":"B105","unstructured":"1994"},{"key":"B106","doi-asserted-by":"publisher","first-page":"e49","DOI":"10.1093\/nar\/gkr1293","article-title":"MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity","volume":"40","author":"Wang","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"B107","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1038\/s41438-020-00391-0","article-title":"A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant","volume":"7","author":"Wei","year":"2020","journal-title":"Hortic Res."},{"key":"B108","doi-asserted-by":"publisher","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci Data"},{"key":"B109","doi-asserted-by":"publisher","first-page":"3978","DOI":"10.1093\/jxb\/erac132","article-title":"The genetic architecture of flowering time changes in pea from wild to crop","volume":"73","author":"Williams","year":"2022","journal-title":"J. Exp. Bot."},{"key":"B110","doi-asserted-by":"publisher","first-page":"1","DOI":"10.46471\/gigabyte.38","article-title":"Chromosome-level assembly of the common vetch (Vicia sativa) reference genome","volume":"2022","author":"Xi","year":"2022","journal-title":"Gigabyte"},{"key":"B111","doi-asserted-by":"publisher","first-page":"1553","DOI":"10.1038\/s41588-022-01172-2","volume":"10","author":"Yang","year":"2022","journal-title":"Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics. Nat Genet."},{"key":"B112","doi-asserted-by":"publisher","first-page":"D996","DOI":"10.1093\/nar\/gkab1007","article-title":"Ensembl Genomes 2022: an expanding genome resource for non-vertebrates","volume":"50","author":"Yates","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"B113","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/j.molp.2020.12.013","article-title":"Orphan crops and their wild relatives in the genomic era","volume":"14","author":"Ye","year":"2021","journal-title":"Mol. Plant"},{"key":"B114","unstructured":"Use of graph database for the integration of heterogeneous biological data19 YoonB. H. KimS-, K. KimS. Y. 10.5808\/GI.2017.15.1.1928416946Genomics Inform152017"},{"key":"B115","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1093\/aob\/mcab083","article-title":"Genetic and gene expression analysis of flowering time regulation by light quality in lentil","volume":"128","author":"Yuan","year":"2021","journal-title":"Annal. Bot."}],"container-title":["Frontiers in Artificial Intelligence"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/frai.2023.1191122\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,25]],"date-time":"2024-10-25T16:50:34Z","timestamp":1729875034000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/frai.2023.1191122\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,8,3]]},"references-count":115,"alternative-id":["10.3389\/frai.2023.1191122"],"URL":"https:\/\/doi.org\/10.3389\/frai.2023.1191122","relation":{},"ISSN":["2624-8212"],"issn-type":[{"value":"2624-8212","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,8,3]]},"article-number":"1191122"}}