Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype data have been collected in many different contexts covering a variety of organisms. The emerging field of phenomics focuses on integrating and interpreting these data to inform biological hypotheses. A major impediment in phenomics is the wide range of distinct and disconnected approaches to recording the observable characteristics of an organism. Phenotype data are collected and curated using free text, single terms or combinations of terms, using multiple vocabularies, terminologies, or ontologies. Integrating these heterogeneous and often siloed data enables the application of biological knowledge both within and across species. Existing integration efforts are typically limited to mappings between pairs of terminologies; a generic knowledge representation that captures the full range of cross-species phenomics data is much needed. We have developed the Unified Phenotype Ontology (uPheno) framework, a community effort to provide an integration layer over domain-specific phenotype ontologies, as a single, unified, logical representation. uPheno comprises (1) a system for consistent computational definition of phenotype terms using ontology design patterns, maintained as a community library; (2) a hierarchical vocabulary of species-neutral phenotype terms under which their species-specific counterparts are grouped; and (3) mapping tables between species-specific ontologies. This harmonized representation supports use cases such as cross-species integration of genotype-phenotype associations from different organisms and cross-species informed variant prioritization.
", "doi": "10.1093/genetics/iyaf027", "issn": "1943-2631", "publisher": "Oxford University Press (OUP)", "publication": "Genetics", "publication_date": "2025-03", "series_number": "3", "volume": "229", "issue": "3", "pages": "iyaf027" }, { "id": "authors:agb38-ew637", "collection": "authors", "collection_id": "agb38-ew637", "cite_using_url": "https://authors.library.caltech.edu/records/agb38-ew637", "type": "article", "title": "Updates to the Alliance of Genome Resources central infrastructure", "author": [ { "family_name": "Aleksander", "given_name": "Suzanne A.", "clpid": "Aleksander-Susanne-A" }, { "family_name": "Anagnostopoulos", "given_name": "Anna V.", "orcid": "0000-0002-6490-7723" }, { "family_name": "Antonazzo", "given_name": "Giulia", "orcid": "0000-0003-0086-5621" }, { "family_name": "Arnaboldi", "given_name": "Valerio", "orcid": "0000-0002-2563-5374", "clpid": "Arnaboldi-Valerio" }, { "family_name": "Attrill", "given_name": "Helen", "orcid": "0000-0003-3212-6364" }, { "family_name": "Becerra", "given_name": "Andr\u00e9s", "orcid": "0000-0001-6038-3427" }, { "family_name": "Bello", "given_name": "Susan M.", "orcid": "0000-0003-4606-0597" }, { "family_name": "Blodgett", "given_name": "Olin" }, { "family_name": "Bradford", "given_name": "Yvonne M.", "orcid": "0000-0002-9900-7880" }, { "family_name": "Bult", "given_name": "Carol J.", "orcid": "0000-0001-9433-210X" }, { "family_name": "Cain", "given_name": "Scott", "orcid": "0000-0003-0459-9607" }, { "family_name": "Calvi", "given_name": "Brian R.", "orcid": "0000-0001-5304-0047" }, { "family_name": "Carbon", "given_name": "Seth", "orcid": "0000-0001-8244-1536" }, { "family_name": "Chan", "given_name": "Juancarlos", "orcid": "0000-0002-7259-8107", "clpid": "Chan-Juancarlos" }, { "family_name": "Chen", "given_name": "Wen J.", "clpid": "Chen-Wen-J" }, { "family_name": "Cherry", "given_name": "J. Michael", "orcid": "0000-0001-9163-5180" }, { "family_name": "Cho", "given_name": "Jaehyoung", "clpid": "Cho-Jaehyoung" }, { "family_name": "Crosby", "given_name": "Madeline A." }, { "family_name": "De Pons", "given_name": "Jeffrey L.", "orcid": "0000-0001-7783-1556" }, { "family_name": "D'Eustachio", "given_name": "Peter", "orcid": "0000-0002-5494-626X" }, { "family_name": "Diamantakis", "given_name": "Stavros", "orcid": "0000-0002-0273-3406" }, { "family_name": "Dolan", "given_name": "Mary E.", "orcid": "0000-0001-7732-3295" }, { "family_name": "dos Santos", "given_name": "Gilberto" }, { "family_name": "Dyer", "given_name": "Sarah", "orcid": "0000-0001-5690-9633" }, { "family_name": "Ebert", "given_name": "Dustin", "orcid": "0000-0002-6659-0416" }, { "family_name": "Engel", "given_name": "Stacia R.", "orcid": "0000-0001-5472-917X" }, { "family_name": "Fashena", "given_name": "David", "orcid": "0000-0001-9656-0683" }, { "family_name": "Fisher", "given_name": "Malcolm", "orcid": "0000-0003-1074-8103" }, { "family_name": "Foley", "given_name": "Saoirse", "orcid": "0000-0002-1791-2837" }, { "family_name": "Gibson", "given_name": "Adam C.", "orcid": "0000-0001-8301-6590" }, { "family_name": "Gollapally", "given_name": "Varun R." }, { "family_name": "Gramates", "given_name": "L. Sian", "orcid": "0000-0002-6700-3797" }, { "family_name": "Grove", "given_name": "Christian A.", "orcid": "0000-0001-9076-6015", "clpid": "Grove-Christian-A" }, { "family_name": "Hale", "given_name": "Paul" }, { "family_name": "Harris", "given_name": "Todd", "orcid": "0000-0003-3406-163X" }, { "family_name": "Hayman", "given_name": "G. Thomas", "orcid": "0000-0002-9553-7227" }, { "family_name": "Hu", "given_name": "Yanhui", "orcid": "0000-0003-1494-1402" }, { "family_name": "James-Zorn", "given_name": "Christina", "orcid": "0000-0001-5495-4588" }, { "family_name": "Karimi", "given_name": "Kamran" }, { "family_name": "Karra", "given_name": "Kalpana", "orcid": "0000-0002-6816-2458" }, { "family_name": "Kishore", "given_name": "Ranjana", "orcid": "0000-0002-1478-7671", "clpid": "Kishore-Ranjana" }, { "family_name": "Kwitek", "given_name": "Anne E.", "orcid": "0000-0003-1024-4116" }, { "family_name": "Laulederkind", "given_name": "Stanley J. F.", "orcid": "0000-0001-5356-4174" }, { "family_name": "Lee", "given_name": "Raymond", "orcid": "0000-0002-8151-7479", "clpid": "Lee-Raymond-Y-N" }, { "family_name": "Longden", "given_name": "Ian" }, { "family_name": "Luypaert", "given_name": "Manuel", "orcid": "0000-0003-3966-849X" }, { "family_name": "Markarian", "given_name": "Nicholas", "orcid": "0000-0003-1347-2392", "clpid": "Markarian-Nicholas" }, { "family_name": "Marygold", "given_name": "Steven J.", "orcid": "0000-0003-2759-266X" }, { "family_name": "Matthews", "given_name": "Beverley", "orcid": "0000-0002-0967-1076" }, { "family_name": "McAndrews", "given_name": "Monica S." }, { "family_name": "Millburn", "given_name": "Gillian", "orcid": "0000-0002-1139-1145" }, { "family_name": "Miyasato", "given_name": "Stuart", "orcid": "0000-0001-5250-8920" }, { "family_name": "Motenko", "given_name": "Howie" }, { "family_name": "Moxon", "given_name": "Sierra", "orcid": "0000-0002-8719-7760" }, { "family_name": "Muller", "given_name": "Hans-Michael", "clpid": "M\u00fcller-Hans-Michael" }, { "family_name": "Mungall", "given_name": "Christopher J.", "orcid": "0000-0002-6601-2165" }, { "family_name": "Muruganujan", "given_name": "Anushya", "orcid": "0000-0001-7169-5864" }, { "family_name": "Mushayahama", "given_name": "Tremayne", "orcid": "0000-0002-2874-6934" }, { "family_name": "Nash", "given_name": "Robert S." }, { "family_name": "Nuin", "given_name": "Paulo" }, { "family_name": "Paddock", "given_name": "Holly" }, { "family_name": "Pells", "given_name": "Troy", "orcid": "0000-0002-2340-5356" }, { "family_name": "Perrimon", "given_name": "Norbert", "orcid": "0000-0001-7542-472X" }, { "family_name": "Pich", "given_name": "Christian", "orcid": "0000-0001-5334-4542" }, { "family_name": "Quinton-Tulloch", "given_name": "Mark", "orcid": "0000-0001-5713-0736" }, { "family_name": "Raciti", "given_name": "Daniela", "orcid": "0000-0002-4945-5837", "clpid": "Raciti-Daniela" }, { "family_name": "Ramachandran", "given_name": "Sridhar", "orcid": "0000-0002-2246-3722" }, { "family_name": "Richardson", "given_name": "Joel E.", "orcid": "0000-0003-3342-5753" }, { "family_name": "Russo Gelbart", "given_name": "Susan" }, { "family_name": "Ruzicka", "given_name": "Leyla", "orcid": "0000-0002-1009-339X" }, { "family_name": "Schindelman", "given_name": "Gary", "clpid": "Schindelman-Gary" }, { "family_name": "Shaw", "given_name": "David R." }, { "family_name": "Sherlock", "given_name": "Gavin", "orcid": "0000-0002-1692-4983" }, { "family_name": "Shrivatsav", "given_name": "Ajay", "orcid": "0000-0003-1741-5141" }, { "family_name": "Singer", "given_name": "Amy", "orcid": "0000-0002-9663-3237" }, { "family_name": "Smith", "given_name": "Constance M.", "orcid": "0000-0001-8915-8557" }, { "family_name": "Smith", "given_name": "Cynthia L.", "orcid": "0000-0003-3691-0324" }, { "family_name": "Smith", "given_name": "Jennifer R." }, { "family_name": "Stein", "given_name": "Lincoln", "orcid": "0000-0002-1983-4588" }, { "family_name": "Sternberg", "given_name": "Paul W", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" }, { "family_name": "Tabone", "given_name": "Christopher J.", "orcid": "0000-0001-8746-0680" }, { "family_name": "Thomas", "given_name": "Paul D.", "orcid": "0000-0002-9074-3507" }, { "family_name": "Thorat", "given_name": "Ketaki", "orcid": "0000-0002-8288-6671" }, { "family_name": "Thota", "given_name": "Jyothi", "orcid": "0000-0003-4482-7627" }, { "family_name": "Tomczuk", "given_name": "Monika", "orcid": "0009-0005-7755-8314" }, { "family_name": "Trovisco", "given_name": "Vitor", "orcid": "0000-0002-8728-0281" }, { "family_name": "Tutaj", "given_name": "Marek A.", "orcid": "0000-0002-1025-101X" }, { "family_name": "Urbano", "given_name": "Jose-Maria", "orcid": "0000-0002-6644-8129" }, { "family_name": "Van Auken", "given_name": "Kimberly", "orcid": "0000-0002-1706-4196", "clpid": "Van-Auken-Kimberly-M" }, { "family_name": "Van Slyke", "given_name": "Ceri E.", "orcid": "0000-0002-2244-7917" }, { "family_name": "Vize", "given_name": "Peter D.", "orcid": "0000-0001-8026-0424" }, { "family_name": "Wang", "given_name": "Qinghua", "clpid": "Wang-Qinghua" }, { "family_name": "Weng", "given_name": "Shuai", "orcid": "0000-0003-4233-0772" }, { "family_name": "Westerfield", "given_name": "Monte", "orcid": "0000-0003-1187-7839" }, { "family_name": "Wilming", "given_name": "Laurens G.", "orcid": "0000-0002-4154-7358" }, { "family_name": "Wong", "given_name": "Edith D.", "orcid": "0000-0001-9799-5523" }, { "family_name": "Wright", "given_name": "Adam", "orcid": "0000-0002-5719-4024" }, { "family_name": "Yook", "given_name": "Karen", "orcid": "0000-0002-4457-6787", "clpid": "Yook-Karen" }, { "family_name": "Zhou", "given_name": "Pinglei", "orcid": "0000-0002-3012-1044" }, { "family_name": "Zorn", "given_name": "Aaron", "orcid": "0000-0003-3217-3590" }, { "family_name": "Zytkovicz", "given_name": "Mark" }, { "literal": "Alliance of Genome Resources Consortium" } ], "abstract": "The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and application programming interfaces (APIs). Here, we focus on developments over the last 2 years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific “landing pages” and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML).
", "doi": "10.1093/genetics/iyae049", "pmcid": "PMC11075569", "issn": "1943-2631", "publisher": "Oxford University Press", "publication": "Genetics", "publication_date": "2024-05", "series_number": "1", "volume": "227", "issue": "1", "pages": "iyae049" }, { "id": "authors:5sbp7-bgs69", "collection": "authors", "collection_id": "5sbp7-bgs69", "cite_using_url": "https://authors.library.caltech.edu/records/5sbp7-bgs69", "type": "article", "title": "WormBase 2024: status and transitioning to Alliance infrastructure", "author": [ { "family_name": "Sternberg", "given_name": "Paul W.", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" }, { "family_name": "Van Auken", "given_name": "Kimberly", "orcid": "0000-0002-1706-4196", "clpid": "Van-Auken-Kimberly-M" }, { "family_name": "Wang", "given_name": "Qinghua", "clpid": "Wang-Qinghua" }, { "family_name": "Wright", "given_name": "Adam", "orcid": "0000-0002-5719-4024" }, { "family_name": "Yook", "given_name": "Karen", "orcid": "0000-0002-4457-6787", "clpid": "Yook-Karen" }, { "family_name": "Zarowiecki", "given_name": "Magdalena", "orcid": "0000-0001-6102-7731" }, { "family_name": "Arnaboldi", "given_name": "Valerio", "orcid": "0000-0002-2563-5374", "clpid": "Arnaboldi-Valerio" }, { "family_name": "Becerra", "given_name": "Andr\u00e9s", "orcid": "0000-0001-6038-3427" }, { "family_name": "Brown", "given_name": "Stephanie", "orcid": "0009-0000-2556-6439" }, { "family_name": "Cain", "given_name": "Scott", "orcid": "0000-0003-0459-9607" }, { "family_name": "Chan", "given_name": "Juancarlos", "orcid": "0000-0002-7259-8107", "clpid": "Chan-Juancarlos" }, { "family_name": "Chen", "given_name": "Wen J." }, { "family_name": "Cho", "given_name": "Jaehyoung" }, { "family_name": "Davis", "given_name": "Paul" }, { "family_name": "Diamantakis", "given_name": "Stavros", "clpid": "0000-0002-0273-3408" }, { "family_name": "Dyer", "given_name": "Sarah", "clpid": "0000-0001-5390-9633" }, { "family_name": "Grigoriadis", "given_name": "Dionysis" }, { "family_name": "Grove", "given_name": "Christian A.", "orcid": "0000-0001-9076-6015", "clpid": "Grove-Christian-A" }, { "family_name": "Harris", "given_name": "Todd", "orcid": "0000-0003-3406-163X" }, { "family_name": "Howe", "given_name": "Kevin", "orcid": "0000-0002-1751-9226" }, { "family_name": "Kishore", "given_name": "Ranjana", "orcid": "0000-0002-1478-7671", "clpid": "Kishore-Ranjana" }, { "family_name": "Lee", "given_name": "Raymond", "orcid": "0000-0002-8151-7479", "clpid": "Lee-Raymond-Y-N" }, { "family_name": "Longden", "given_name": "Ian" }, { "family_name": "Luypaert", "given_name": "Manuel", "orcid": "0000-0003-3966-849X" }, { "family_name": "M\u00fcller", "given_name": "Hans-Michael", "clpid": "M\u00fcller-Hans-Michael" }, { "family_name": "Nuin", "given_name": "Paulo" }, { "family_name": "Quinton-Tulloch", "given_name": "Mark", "orcid": "0000-0001-5713-0736" }, { "family_name": "Raciti", "given_name": "Daniela", "orcid": "0000-0002-4945-5837", "clpid": "Raciti-Daniela" }, { "family_name": "Schedl", "given_name": "Tim", "orcid": "0000-0003-2148-2996" }, { "family_name": "Schindelman", "given_name": "Gary", "clpid": "Schindelman-Gary-C" }, { "family_name": "Stein", "given_name": "Lincoln", "orcid": "0000-0002-1983-4588" } ], "abstract": "WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-paced C. elegans research, to provide better integration with other resources, and to be sustainable. Here, we discuss the current state of WormBase as well as progress and plans for moving core WormBase infrastructure to the Alliance of Genome Resources (the Alliance). As an Alliance member, WormBase will continue to interact with the C. elegans community, develop new features as needed, and curate key information from the literature and large-scale projects.
", "doi": "10.1093/genetics/iyae050", "pmcid": "PMC11075546", "issn": "1943-2631", "publisher": "Oxford University Press", "publication": "Genetics", "publication_date": "2024-05", "series_number": "1", "volume": "227", "issue": "1", "pages": "iyae050" }, { "id": "authors:r7yym-m0j48", "collection": "authors", "collection_id": "r7yym-m0j48", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220406-521823507", "type": "article", "title": "Harmonizing model organism data in the Alliance of Genome Resources", "author": [ { "family_name": "Agapite", "given_name": "Julie", "clpid": "Agapite-Julie" }, { "family_name": "Albou", "given_name": "Laurent-Philippe", "orcid": "0000-0001-5801-1974" }, { "family_name": "Aleksander", "given_name": "Suzanne A." }, { "family_name": "Alexander", "given_name": "Micheal" }, { "family_name": "Anagnostopoulos", "given_name": "Anna V." }, { "family_name": "Antonazzo", "given_name": "Giulia" }, { "family_name": "Argasinska", "given_name": "Joanna" }, { "family_name": "Arnaboldi", "given_name": "Valerio", "orcid": "0000-0002-2563-5374", "clpid": "Arnaboldi-Valerio" }, { "family_name": "Attrill", "given_name": "Helen", "orcid": "0000-0003-3212-6364" }, { "family_name": "Becerra", "given_name": "Andr\u00e9s" }, { "family_name": "Bello", "given_name": "Susan M." }, { "family_name": "Blake", "given_name": "Judith A.", "orcid": "0000-0001-8522-334X" }, { "family_name": "Blodgett", "given_name": "Olin" }, { "family_name": "Bradford", "given_name": "Yvonne M." }, { "family_name": "Bult", "given_name": "Carol J." }, { "family_name": "Cain", "given_name": "Scott" }, { "family_name": "Calvi", "given_name": "Brian R." }, { "family_name": "Carbon", "given_name": "Seth", "orcid": "0000-0001-8244-1536" }, { "family_name": "Chan", "given_name": "Juancarlos", "orcid": "0000-0002-7259-8107", "clpid": "Chan-Juancarlos-N" }, { "family_name": "Chen", "given_name": "Wen J.", "clpid": "Chen-Wen-J" }, { "family_name": "Cherry", "given_name": "J. Michael", "orcid": "0000-0001-9163-5180" }, { "family_name": "Cho", "given_name": "Jaehyoung", "clpid": "Cho-Jaehyoung" }, { "family_name": "Christie", "given_name": "Karen R." }, { "family_name": "Crosby", "given_name": "Madeline A." }, { "family_name": "Davis", "given_name": "Paul", "orcid": "0000-0001-5545-0824" }, { "family_name": "da Veiga Beltrame", "given_name": "Eduardo", "orcid": "0000-0002-1529-9207", "clpid": "da-Veiga-Beltrame-Eduardo" }, { "family_name": "De Pons", "given_name": "Jeffrey L." }, { "family_name": "D'Eustachio", "given_name": "Peter", "orcid": "0000-0002-5494-626X" }, { "family_name": "Diamantakis", "given_name": "Stavros" }, { "family_name": "Dolan", "given_name": "Mary E.", "orcid": "0000-0001-7732-3295" }, { "family_name": "dos Santos", "given_name": "Gilberto" }, { "family_name": "Douglass", "given_name": "Eric" }, { "family_name": "Dunn", "given_name": "Barbara" }, { "family_name": "Eagle", "given_name": "Anne" }, { "family_name": "Ebert", "given_name": "Dustin" }, { "family_name": "Engel", "given_name": "Stacia R.", "orcid": "0000-0001-5472-917X" }, { "family_name": "Fashena", "given_name": "David" }, { "family_name": "Foley", "given_name": "Saoirse", "orcid": "0000-0002-1791-2837" }, { "family_name": "Frazer", "given_name": "Ken" }, { "family_name": "Gao", "given_name": "Sibyl" }, { "family_name": "Gibson", "given_name": "Adam C." }, { "family_name": "Gondwe", "given_name": "Felix" }, { "family_name": "Goodman", "given_name": "Josh" }, { "family_name": "Gramates", "given_name": "L. Sian" }, { "family_name": "Grove", "given_name": "Christian A.", "orcid": "0000-0001-9076-6015", "clpid": "Grove-Christian-A" }, { "family_name": "Hale", "given_name": "Paul" }, { "family_name": "Harris", "given_name": "Todd", "orcid": "0000-0003-3406-163X" }, { "family_name": "Thomas Hayman", "given_name": "G." }, { "family_name": "Hill", "given_name": "David P.", "orcid": "0000-0001-7476-6306" }, { "family_name": "Howe", "given_name": "Douglas G." }, { "family_name": "Howe", "given_name": "Kevin L.", "orcid": "0000-0002-1751-9226" }, { "family_name": "Hu", "given_name": "Yanhui" }, { "family_name": "Jha", "given_name": "Sagar" }, { "family_name": "Kadin", "given_name": "James A." }, { "family_name": "Kaufman", "given_name": "Thomas C." }, { "family_name": "Kalita", "given_name": "Patrick" }, { "family_name": "Karra", "given_name": "Kalpana" }, { "family_name": "Kishore", "given_name": "Ranjana", "orcid": "0000-0002-1478-7671", "clpid": "Kishore-Ranjana" }, { "family_name": "Kwitek", "given_name": "Anne E." }, { "family_name": "Laulederkind", "given_name": "Stanley J. F." }, { "family_name": "Lee", "given_name": "Raymond", "orcid": "0000-0002-8151-7479", "clpid": "Lee-Raymond-Y-N" }, { "family_name": "Longden", "given_name": "Ian" }, { "family_name": "Luypaert", "given_name": "Manuel", "orcid": "0000-0003-3966-849X" }, { "family_name": "MacPherson", "given_name": "Kevin A." }, { "family_name": "Martin", "given_name": "Ryan" }, { "family_name": "Marygold", "given_name": "Steven J." }, { "family_name": "Matthews", "given_name": "Beverley" }, { "family_name": "McAndrews", "given_name": "Monica S." }, { "family_name": "Millburn", "given_name": "Gillian" }, { "family_name": "Miyasato", "given_name": "Stuart" }, { "family_name": "Motenko", "given_name": "Howie" }, { "family_name": "Moxon", "given_name": "Sierra" }, { "family_name": "M\u00fcller", "given_name": "Hans-Michael", "clpid": "M\u00fcller-Hans-Michael" }, { "family_name": "Mungall", "given_name": "Christopher J.", "orcid": "0000-0002-6601-2165" }, { "family_name": "Muruganujan", "given_name": "Anushya" }, { "family_name": "Mushayahama", "given_name": "Tremayne" }, { "family_name": "Nalabolu", "given_name": "Harika S." }, { "family_name": "Nash", "given_name": "Robert S." }, { "family_name": "Ng", "given_name": "Patrick" }, { "family_name": "Nuin", "given_name": "Paulo", "orcid": "0000-0003-4915-664X" }, { "family_name": "Paddock", "given_name": "Holly" }, { "family_name": "Paulini", "given_name": "Michael", "orcid": "0000-0002-6968-2340" }, { "family_name": "Perrimon", "given_name": "Norbert" }, { "family_name": "Pich", "given_name": "Christian" }, { "family_name": "Quinton-Tulloch", "given_name": "Mark", "orcid": "0000-0001-5713-0736" }, { "family_name": "Raciti", "given_name": "Daniela", "clpid": "Raciti-Daniela" }, { "family_name": "Ramachandran", "given_name": "Sridhar" }, { "family_name": "Richardson", "given_name": "Joel E." }, { "family_name": "Russo Gelbart", "given_name": "Susan" }, { "family_name": "Ruzicka", "given_name": "Leyla" }, { "family_name": "Schaper", "given_name": "Kevin" }, { "family_name": "Schindelman", "given_name": "Gary", "clpid": "Schindelman-Gary" }, { "family_name": "Shimoyama", "given_name": "Mary" }, { "family_name": "Simison", "given_name": "Matt" }, { "family_name": "Shaw", "given_name": "David R." }, { "family_name": "Shrivatsav", "given_name": "Ajay" }, { "family_name": "Singer", "given_name": "Amy" }, { "family_name": "Skrzypek", "given_name": "Marek" }, { "family_name": "Smith", "given_name": "Constance M." }, { "family_name": "Smith", "given_name": "Cynthia L." }, { "family_name": "Smith", "given_name": "Jennifer R." }, { "family_name": "Stein", "given_name": "Lincoln" }, { "family_name": "Sternberg", "given_name": "Paul W.", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" }, { "family_name": "Tabone", "given_name": "Christopher J." }, { "family_name": "Thomas", "given_name": "Paul D.", "orcid": "0000-0002-9074-3507" }, { "family_name": "Thorat", "given_name": "Ketaki" }, { "family_name": "Thota", "given_name": "Jyothi" }, { "family_name": "Toro", "given_name": "Sabrina" }, { "family_name": "Tomczuk", "given_name": "Monika" }, { "family_name": "Trovisco", "given_name": "Vitor" }, { "family_name": "Tutaj", "given_name": "Marek A." }, { "family_name": "Tutaj", "given_name": "Monika" }, { "family_name": "Urbano", "given_name": "Jose-Maria" }, { "family_name": "Van Auken", "given_name": "Kimberly", "orcid": "0000-0002-1706-4196", "clpid": "Van-Auken-Kimberly-M" }, { "family_name": "Van Slyke", "given_name": "Ceri E.", "orcid": "0000-0002-2244-7917" }, { "family_name": "Wang", "given_name": "Qinghua", "clpid": "Wang-Qinghua" }, { "family_name": "Wang", "given_name": "Shur-Jen" }, { "family_name": "Weng", "given_name": "Shuai" }, { "family_name": "Westerfield", "given_name": "Monte" }, { "family_name": "Williams", "given_name": "Gary" }, { "family_name": "Wilming", "given_name": "Laurens G." }, { "family_name": "Wong", "given_name": "Edith D." }, { "family_name": "Wright", "given_name": "Adam", "orcid": "0000-0002-5719-4024" }, { "family_name": "Yook", "given_name": "Karen", "orcid": "0000-0002-4457-6787", "clpid": "Yook-Karen-J" }, { "family_name": "Zarowiecki", "given_name": "Magdalena", "orcid": "0000-0001-6102-7731" }, { "family_name": "Zhou", "given_name": "Pinglei" }, { "family_name": "Zytkovicz", "given_name": "Mark" }, { "literal": "Alliance of Genome Resources Consortium" } ], "abstract": "The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein\u2013protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.", "doi": "10.1093/genetics/iyac022", "pmcid": "PMC8982023", "issn": "1943-2631", "publisher": "Oxford University Press", "publication": "Genetics", "publication_date": "2022-04", "series_number": "4", "volume": "220", "issue": "4", "pages": "Art. No. iyac022" }, { "id": "authors:ax9qa-w5481", "collection": "authors", "collection_id": "ax9qa-w5481", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220310-752284000", "type": "article", "title": "WormBase in 2022\u2014data, processes, and tools for analyzing Caenorhabditis elegans", "author": [ { "family_name": "Davis", "given_name": "Paul", "orcid": "0000-0001-5545-0824", "clpid": "Davis-Paul" }, { "family_name": "Zarowiecki", "given_name": "Magdalena", "orcid": "0000-0001-6102-7731" }, { "family_name": "Arnaboldi", "given_name": "Valerio", "orcid": "0000-0002-2563-5374", "clpid": "Arnaboldi-Valerio" }, { "family_name": "Becerra", "given_name": "Andr\u00e9s" }, { "family_name": "Cain", "given_name": "Scott" }, { "family_name": "Chan", "given_name": "Juancarlos", "orcid": "0000-0002-7259-8107", "clpid": "Chan-Juancarlos-N" }, { "family_name": "Chen", "given_name": "Wen J.", "clpid": "Chen-Wen-J" }, { "family_name": "Cho", "given_name": "Jaehyoung", "clpid": "Cho-Jaehyoung" }, { "family_name": "da Veiga Beltrame", "given_name": "Eduardo", "orcid": "0000-0002-1529-9207", "clpid": "da-Veiga-Beltrame-Eduardo" }, { "family_name": "Diamantakis", "given_name": "Stavros" }, { "family_name": "Gao", "given_name": "Sibyl" }, { "family_name": "Grigoriadis", "given_name": "Dionysis" }, { "family_name": "Grove", "given_name": "Christian A.", "orcid": "0000-0001-9076-6015", "clpid": "Grove-Christian-A" }, { "family_name": "Harris", "given_name": "Todd W.", "orcid": "0000-0003-3406-163X" }, { "family_name": "Kishore", "given_name": "Ranjana", "orcid": "0000-0002-1478-7671", "clpid": "Kishore-Ranjana" }, { "family_name": "Le", "given_name": "Tuan" }, { "family_name": "Lee", "given_name": "Raymond Y. N.", "orcid": "0000-0002-8151-7479", "clpid": "Lee-Raymond-Y-N" }, { "family_name": "Luypaert", "given_name": "Manuel", "orcid": "0000-0003-3966-849X" }, { "family_name": "M\u00fcller", "given_name": "Hans-Michael", "clpid": "M\u00fcller-Hans-Michael" }, { "family_name": "Nakamura", "given_name": "Cecilia", "orcid": "0000-0002-4689-7314", "clpid": "Nakamura-Cecilia" }, { "family_name": "Nuin", "given_name": "Paulo", "orcid": "0000-0003-4915-664X" }, { "family_name": "Paulini", "given_name": "Michael", "orcid": "0000-0002-6968-2340" }, { "family_name": "Quinton-Tulloch", "given_name": "Mark", "orcid": "0000-0001-5713-0736" }, { "family_name": "Raciti", "given_name": "Daniela", "clpid": "Raciti-Daniela" }, { "family_name": "Rodgers", "given_name": "Faye H.", "orcid": "0000-0003-2391-9573" }, { "family_name": "Russell", "given_name": "Matthew", "orcid": "0000-0001-6140-6723" }, { "family_name": "Schindelman", "given_name": "Gary", "clpid": "Schindelman-Gary" }, { "family_name": "Singh", "given_name": "Archana", "orcid": "0000-0002-5027-4582" }, { "family_name": "Stickland", "given_name": "Tim", "orcid": "0000-0003-3185-1433" }, { "family_name": "Van Auken", "given_name": "Kimberly", "orcid": "0000-0002-1706-4196", "clpid": "Van-Auken-Kimberly" }, { "family_name": "Wang", "given_name": "Qinghua", "clpid": "Wang-Qinghua" }, { "family_name": "Williams", "given_name": "Gary" }, { "family_name": "Wright", "given_name": "Adam J.", "orcid": "0000-0002-5719-4024" }, { "family_name": "Yook", "given_name": "Karen", "orcid": "0000-0002-4457-6787", "clpid": "Yook-Karen-J" }, { "family_name": "Berriman", "given_name": "Matt", "orcid": "0000-0002-9581-0377" }, { "family_name": "Howe", "given_name": "Kevin L.", "orcid": "0000-0002-1751-9226" }, { "family_name": "Schedl", "given_name": "Tim", "orcid": "0000-0003-2148-2996" }, { "family_name": "Stein", "given_name": "Lincoln", "orcid": "0000-0002-1983-4588" }, { "family_name": "Sternberg", "given_name": "Paul W.", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" } ], "abstract": "WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member.", "doi": "10.1093/genetics/iyac003", "pmcid": "PMC8982018", "issn": "1943-2631", "publisher": "Oxford University Press", "publication": "Genetics", "publication_date": "2022-04", "series_number": "4", "volume": "220", "issue": "4", "pages": "Art. No. iyac003" }, { "id": "authors:jfhsd-n5y51", "collection": "authors", "collection_id": "jfhsd-n5y51", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210422-070627594", "type": "article", "title": "Student Annotations of Published Data as a Collaboration between an Online Laboratory Course and the C. elegans Database, WormBase", "author": [ { "family_name": "Dahlberg", "given_name": "Caroline L.", "orcid": "0000-0001-6940-4888", "clpid": "Dahlberg-Caroline-L" }, { "family_name": "Grove", "given_name": "Christian A.", "orcid": "0000-0001-9076-6015", "clpid": "Grove-Christian-A" }, { "family_name": "Hulsey-Vincent", "given_name": "Heino", "clpid": "Hulsey-Vincent-Heino" }, { "family_name": "Ismail", "given_name": "Samiya", "clpid": "Ismail-Samiya" } ], "abstract": "Course-based undergraduate research experiences (CUREs) provide the same benefits as individual, mentored faculty research while expanding the availability of research opportunities. One important aspect of CUREs is students' engagement in collaboration. The shift to online learning during the COVID-19 pandemic created an immediate need for meaningful, collaborative experiences in CUREs. We developed a partnership with the Caenorhabditis elegans (C. elegans) database, WormBase, in which students submitted annotations of published manuscripts to the website. Due to the stress on students during this time of crisis, qualitative data were collected in lieu of quantitative pre- and postanalyses. Most students reported on cognitive processes that represent mid-level Bloom's categories. By partnering with WormBase, students gained insight into the scientific community and contributed as community members. We describe possible modifications for future courses, potential expansion of the WormBase collaboration, and future directions for quantitative analysis.", "doi": "10.1128/jmbe.v22i1.2331", "pmcid": "PMC8012049", "issn": "1935-7877", "publisher": "American Society for Microbiology", "publication": "Journal of Microbiology and Biology Education", "publication_date": "2021-03-31", "series_number": "1", "volume": "22", "issue": "1", "pages": "1-11" }, { "id": "authors:vk9jd-bna77", "collection": "authors", "collection_id": "vk9jd-bna77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210210-070215975", "type": "article", "title": "Gene Ontology resource: enriching a GOld mine", "author": [ { "family_name": "Carbon", "given_name": "Seth", "orcid": "0000-0001-8244-1536", "clpid": "Carbon-Seth" }, { "family_name": "Douglass", "given_name": "Eric" }, { "family_name": "Good", "given_name": "Benjamin M." }, { "family_name": "Unni", "given_name": "Deepak R." }, { "family_name": "Harris", "given_name": "Nomi L." }, { "family_name": "Mungall", "given_name": "Christopher J.", "orcid": "0000-0002-6601-2165" }, { "family_name": "Basu", "given_name": "Siddartha" }, { "family_name": "Chisholm", "given_name": "Rex L." }, { "family_name": "Dodson", "given_name": "Robert J." }, { "family_name": "Hartline", "given_name": "Eric" }, { "family_name": "Fey", "given_name": "Petra" }, { "family_name": "Thomas", "given_name": "Paul D.", "orcid": "0000-0002-9074-3507" }, { "family_name": "Albou", "given_name": "Laurent-Philippe", "orcid": "0000-0001-5801-1974" }, { "family_name": "Ebert", "given_name": "Dustin" }, { "family_name": "Kesling", "given_name": "Michael J." }, { "family_name": "Mi", "given_name": "Huaiyu", "orcid": "0000-0001-8721-202X" }, { "family_name": "Muruganujan", "given_name": "Anushya" }, { "family_name": "Huang", "given_name": "Xiaosong" }, { "family_name": "Mushayahama", "given_name": "Tremayne" }, { "family_name": "LaBonte", "given_name": "Sandra A." }, { "family_name": "Siegele", "given_name": "Deborah A." }, { "family_name": "Antonazzo", "given_name": "Giulia" }, { "family_name": "Attrill", "given_name": "Helen", "orcid": "0000-0003-3212-6364" }, { "family_name": "Brown", "given_name": "Nick H." }, { "family_name": "Garapati", "given_name": "Phani" }, { "family_name": "Marygold", "given_name": "Steven J." }, { "family_name": "Trovisco", "given_name": "Vitor" }, { "family_name": "dos Santos", "given_name": "Gil" }, { "family_name": "Falls", "given_name": "Kathleen" }, { "family_name": "Tabone", "given_name": "Christopher" }, { "family_name": "Zhou", "given_name": "Pinglei" }, { "family_name": "Goodman", "given_name": "Joshua L." }, { "family_name": "Strelets", "given_name": "Victor B." }, { "family_name": "Thurmond", "given_name": "Jim" }, { "family_name": "Garmiri", "given_name": "Penelope" }, { "family_name": "Ishtiaq", "given_name": "Rizwan" }, { "family_name": "Rodr\u00edguez-L\u00f3pez", "given_name": "Milagros" }, { "family_name": "Acencio", "given_name": "Marcio L." }, { "family_name": "Kuiper", "given_name": "Martin" }, { "family_name": "L\u00e6greid", "given_name": "Astrid" }, { "family_name": "Logie", "given_name": "Colin" }, { "family_name": "Lovering", "given_name": "Ruth C.", "orcid": "0000-0002-9791-0064" }, { "family_name": "Kramarz", "given_name": "Barbara" }, { "family_name": "Saverimuttu", "given_name": "Shirin C. C." }, { "family_name": "Pinheiro", "given_name": "Sandra M." }, { "family_name": "Gunn", "given_name": "Heather" }, { "family_name": "Su", "given_name": "Renzhi" }, { "family_name": "Thurlow", "given_name": "Katherine E." }, { "family_name": "Chibucos", "given_name": "Marcus C.", "orcid": "0000-0001-9586-0780" }, { "family_name": "Giglio", "given_name": "Michelle", "orcid": "0000-0001-7628-5565" }, { "family_name": "Nadendla", "given_name": "Suvarna" }, { "family_name": "Munro", "given_name": "James" }, { "family_name": "Jackson", "given_name": "Rebecca" }, { "family_name": "Duesbury", "given_name": "Margaret J." }, { "family_name": "Del-Toro", "given_name": "Noemi" }, { "family_name": "Meldal", "given_name": "Birgit H. M." }, { "family_name": "Paneerselvam", "given_name": "Kalpana" }, { "family_name": "Perfetto", "given_name": "Livia" }, { "family_name": "Porras", "given_name": "Pablo" }, { "family_name": "Orchard", "given_name": "Sandra" }, { "family_name": "Shrivastava", "given_name": "Anjali" }, { "family_name": "Chang", "given_name": "Hsin-Yu" }, { "family_name": "Finn", "given_name": "Robert Daniel" }, { "family_name": "Mitchell", "given_name": "Alexander Lawson" }, { "family_name": "Rawlings", "given_name": "Neil David" }, { "family_name": "Richardson", "given_name": "Lorna" }, { "family_name": "Sangrador-Vegas", "given_name": "Amaia" }, { "family_name": "Blake", "given_name": "Judith A." }, { "family_name": "Christie", "given_name": "Karen R." }, { "family_name": "Dolan", "given_name": "Mary E.", "orcid": "0000-0001-7732-3295" }, { "family_name": "Drabkin", "given_name": "Harold J." }, { "family_name": "Hill", "given_name": "David P.", "orcid": "0000-0001-7476-6306" }, { "family_name": "Ni", "given_name": "Li" }, { "family_name": "Sitnikov", "given_name": "Dmitry M." }, { "family_name": "Harris", "given_name": "Midori A.", "orcid": "0000-0003-4148-4606" }, { "family_name": "Oliver", "given_name": "Stephen G." }, { "family_name": "Rutherford", "given_name": "Kim M.", "orcid": "0000-0001-6277-726X" }, { "family_name": "Wood", "given_name": "Valerie", "orcid": "0000-0001-6330-7526" }, { "family_name": "Hayles", "given_name": "Jaqueline" }, { "family_name": "B\u00e4hler", "given_name": "J\u00fcrg" }, { "family_name": "Bolton", "given_name": "Elizabeth R." }, { "family_name": "De Pons", "given_name": "Jeffery L." }, { "family_name": "Dwinell", "given_name": "Melinda R." }, { "family_name": "Hayman", "given_name": "G. Thomas" }, { "family_name": "Kaldunski", "given_name": "Mary L." }, { "family_name": "Kwitek", "given_name": "Anne E." }, { "family_name": "Laulederkind", "given_name": "Stanley J. F." }, { "family_name": "Plasterer", "given_name": "Cody" }, { "family_name": "Tutaj", "given_name": "Marek A." }, { "family_name": "Vedi", "given_name": "Mahima" }, { "family_name": "Wang", "given_name": "Shur-Jen" }, { "family_name": "D'Eustachio", "given_name": "Peter" }, { "family_name": "Matthews", "given_name": "Lisa" }, { "family_name": "Balhoff", "given_name": "James P.", "orcid": "0000-0002-8688-6599" }, { "family_name": "Aleksander", "given_name": "Suzi A." }, { "family_name": "Alexander", "given_name": "Michael J." }, { "family_name": "Cherry", "given_name": "J. Michael", "orcid": "0000-0001-9163-5180" }, { "family_name": "Engel", "given_name": "Stacia R.", "orcid": "0000-0001-5472-917X" }, { "family_name": "Gondwe", "given_name": "Felix" }, { "family_name": "Karra", "given_name": "Kalpana" }, { "family_name": "Miyasato", "given_name": "Stuart R." }, { "family_name": "Nash", "given_name": "Robert S." }, { "family_name": "Simison", "given_name": "Matt" }, { "family_name": "Skrzypek", "given_name": "Marek S." }, { "family_name": "Weng", "given_name": "Shuai" }, { "family_name": "Wong", "given_name": "Edith D." }, { "family_name": "Feuermann", "given_name": "Marc", "orcid": "0000-0002-4187-2863" }, { "family_name": "Gaudet", "given_name": "Pascale", "orcid": "0000-0003-1813-6857" }, { "family_name": "Morgat", "given_name": "Anne" }, { "family_name": "Bakker", "given_name": "Erica" }, { "family_name": "Berardini", "given_name": "Tanya Z." }, { "family_name": "Reiser", "given_name": "Leonore", "orcid": "0000-0003-0073-0858" }, { "family_name": "Subramaniam", "given_name": "Shabari" }, { "family_name": "Huala", "given_name": "Eva" }, { "family_name": "Arighi", "given_name": "Cecilia N." }, { "family_name": "Auchincloss", "given_name": "Andrea" }, { "family_name": "Axelsen", "given_name": "Kristian" }, { "family_name": "Argoud-Puy", "given_name": "Ghislaine" }, { "family_name": "Bateman", "given_name": "Alex", "orcid": "0000-0002-6982-4660" }, { "family_name": "Blatter", "given_name": "Marie-Claude" }, { "family_name": "Boutet", "given_name": "Emmanuel" }, { "family_name": "Bowler", "given_name": "Emily" }, { "family_name": "Breuza", "given_name": "Lionel" }, { "family_name": "Bridge", "given_name": "Alan" }, { "family_name": "Britto", "given_name": "Ramona" }, { "family_name": "Bye-A-Jee", "given_name": "Hema" }, { "family_name": "Casals Casas", "given_name": "Cristina" }, { "family_name": "Coudert", "given_name": "Elisabeth" }, { "family_name": "Denny", "given_name": "Paul" }, { "family_name": "Estreicher", "given_name": "Anne" }, { "family_name": "Famiglietti", "given_name": "Maria Livia" }, { "family_name": "Georghiou", "given_name": "George", "orcid": "0000-0001-5067-3199" }, { "family_name": "Gos", "given_name": "Arnaud" }, { "family_name": "Gruaz-Gumowski", "given_name": "Nadine" }, { "family_name": "Hatton-Ellis", "given_name": "Emma" }, { "family_name": "Hulo", "given_name": "Chantal" }, { "family_name": "Ignatchenko", "given_name": "Alexandr" }, { "family_name": "Jungo", "given_name": "Florence" }, { "family_name": "Laiho", "given_name": "Kati" }, { "family_name": "Le Mercier", "given_name": "Philippe" }, { "family_name": "Lieberherr", "given_name": "Damien" }, { "family_name": "Lock", "given_name": "Antonia", "orcid": "0000-0003-1179-5999" }, { "family_name": "Lussi", "given_name": "Yvonne" }, { "family_name": "MacDougall", "given_name": "Alistair" }, { "family_name": "Magrane", "given_name": "Michele" }, { "family_name": "Martin", "given_name": "Maria J." }, { "family_name": "Masson", "given_name": "Patrick" }, { "family_name": "Natale", "given_name": "Darren A." }, { "family_name": "Hyka-Nouspikel", "given_name": "Nevila" }, { "family_name": "Orchard", "given_name": "Sandra" }, { "family_name": "Pedruzzi", "given_name": "Ivo" }, { "family_name": "Pourcel", "given_name": "Lucille" }, { "family_name": "Poux", "given_name": "Sylvain", "orcid": "0000-0001-7299-6685" }, { "family_name": "Pundir", "given_name": "Sangya" }, { "family_name": "Rivoire", "given_name": "Catherine" }, { "family_name": "Speretta", "given_name": "Elena" }, { "family_name": "Sundaram", "given_name": "Shyamala" }, { "family_name": "Tyagi", "given_name": "Nidhi" }, { "family_name": "Warner", "given_name": "Kate" }, { "family_name": "Zaru", "given_name": "Rossana" }, { "family_name": "Wu", "given_name": "Cathy H." }, { "family_name": "Diehl", "given_name": "Alexander D." }, { "family_name": "Chan", "given_name": "Juancarlos N.", "orcid": "0000-0002-7259-8107", "clpid": "Chan-Juancarlos-N" }, { "family_name": "Grove", "given_name": "Christian", "orcid": "0000-0001-9076-6015", "clpid": "Grove-Christian-A" }, { "family_name": "Lee", "given_name": "Raymond Y. N.", "orcid": "0000-0002-8151-7479", "clpid": "Lee-Raymond-Y-N" }, { "family_name": "M\u00fcller", "given_name": "Hans-Michael", "clpid": "M\u00fcller-Hans-Michael" }, { "family_name": "Raciti", "given_name": "Daniela", "clpid": "Raciti-Daniela" }, { "family_name": "Van Auken", "given_name": "Kimberly", "orcid": "0000-0002-1706-4196", "clpid": "Van-Auken-Kimberly" }, { "family_name": "Sternberg", "given_name": "Paul W.", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" }, { "family_name": "Berriman", "given_name": "Matthew", "orcid": "0000-0002-9581-0377" }, { "family_name": "Paulini", "given_name": "Michael" }, { "family_name": "Howe", "given_name": "Kevin", "orcid": "0000-0002-1751-9226" }, { "family_name": "Gao", "given_name": "Sibyl" }, { "family_name": "Wright", "given_name": "Adam" }, { "family_name": "Stein", "given_name": "Lincoln", "orcid": "0000-0002-1983-4588" }, { "family_name": "Howe", "given_name": "Douglas G." }, { "family_name": "Toro", "given_name": "Sabrina" }, { "family_name": "Westerfield", "given_name": "Monte" }, { "family_name": "Jaiswal", "given_name": "Pankaj" }, { "family_name": "Cooper", "given_name": "Laurel" }, { "family_name": "Elser", "given_name": "Justin" }, { "literal": "Gene Ontology Consortium" } ], "abstract": "The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.", "doi": "10.1093/nar/gkaa1113", "pmcid": "PMC7779012", "issn": "0305-1048", "publisher": "Oxford University Press", "publication": "Nucleic Acids Research", "publication_date": "2021-01-08", "series_number": "D1", "volume": "49", "issue": "D1", "pages": "D325-D334" }, { "id": "authors:scabh-anq11", "collection": "authors", "collection_id": "scabh-anq11", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191029-103634272", "type": "article", "title": "WormBase: a modern Model Organism Information Resource", "author": [ { "family_name": "Harris", "given_name": "Todd W.", "orcid": "0000-0003-3406-163X", "clpid": "Harris-Todd-W" }, { "family_name": "Arnaboldi", "given_name": "Valerio", "orcid": "0000-0002-2563-5374", "clpid": "Arnaboldi-Valerio" }, { "family_name": "Chan", "given_name": "Juancarlos", "orcid": "0000-0002-7259-8107", "clpid": "Chan-Juancarlos" }, { "family_name": "Chen", "given_name": "Wen J.", "clpid": "Chen-Wen-J" }, { "family_name": "Cho", "given_name": "Jaehyoung", "clpid": "Cho-Jaehyoung" }, { "family_name": "Grove", "given_name": "Christian A.", "orcid": "0000-0001-9076-6015", "clpid": "Grove-Christian-A" }, { "family_name": "Kishore", "given_name": "Ranjana", "clpid": "Kishore-Ranjana" }, { "family_name": "Lee", "given_name": "Y. N.", "orcid": "0000-0002-8151-7479", "clpid": "Lee-Raymond-Y-N" }, { "family_name": "M\u00fcller", "given_name": "Hans-Michael", "clpid": "M\u00fcller-Hans-Michael" }, { "family_name": "Nakamura", "given_name": "Cecilia", "orcid": "0000-0002-4689-7314", "clpid": "Nakamura-Cecilia" }, { "family_name": "Raciti", "given_name": "Daniela", "clpid": "Raciti-Daniela" }, { "family_name": "Schindelman", "given_name": "Gary", "clpid": "Schindelman-Gary" }, { "family_name": "V. Auken", "given_name": "Kimberly", "orcid": "0000-0002-1706-4196", "clpid": "Van-Auken-K" }, { "family_name": "Wang", "given_name": "Qinghua", "clpid": "Wang-Qinghua" }, { "family_name": "Yook", "given_name": "Karen", "orcid": "0000-0002-4457-6787", "clpid": "Yook-Karen-J" }, { "family_name": "Sternberg", "given_name": "Paul W.", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" } ], "abstract": "WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user interface and architecture. In this update, we describe progress in each of these three areas. In particular, we discuss the status of literature curation and recently added data, detail new features of the web interface and options for users wishing to conduct data mining workflows, and discuss our efforts to build a robust and scalable architecture by leveraging commercial cloud offerings. We conclude with a description of WormBase's role as a founding member of the nascent Alliance of Genome Resources.", "doi": "10.1093/nar/gkz920", "pmcid": "PMC7145598", "issn": "0305-1048", "publisher": "Oxford University Press", "publication": "Nucleic Acids Research", "publication_date": "2020-01-08", "series_number": "D1", "volume": "48", "issue": "D1", "pages": "D762-D767" }, { "id": "authors:6zgfv-edt58", "collection": "authors", "collection_id": "6zgfv-edt58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191111-110405748", "type": "article", "title": "The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species", "author": [ { "family_name": "Shefchek", "given_name": "Kent A.", "orcid": "0000-0001-6439-2224", "clpid": "Shefchek-Kent-A" }, { "family_name": "Grove", "given_name": "Chris", "orcid": "0000-0001-9076-6015", "clpid": "Grove-Christian-A" } ], "abstract": "In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven't been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources must be queried to find potentially significant phenotypic associations. The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search. We develop many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases. Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research. Launched in 2015, Monarch has grown with regards to data (new organisms, more sources, better modeling); new API and standards; ontologies (new Mondo unified disease ontology, improvements to ontologies such as HPO and uPheno); user interface (a redesigned website); and community development. Monarch data, algorithms and tools are being used and extended by resources such as GA4GH and NCATS Translator, among others, to aid mechanistic discovery and diagnostics.", "doi": "10.1093/nar/gkz997", "pmcid": "PMC7056945", "issn": "0305-1048", "publisher": "Oxford University Press", "publication": "Nucleic Acids Research", "publication_date": "2020-01-08", "series_number": "D1", "volume": "48", "issue": "D1", "pages": "D704-D715" }, { "id": "authors:bb1ps-94z46", "collection": "authors", "collection_id": "bb1ps-94z46", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200629-072302491", "type": "article", "title": "2018 Update on Protein-Protein Interaction Data in WormBase", "author": [ { "family_name": "Cho", "given_name": "Jaehyoung", "clpid": "Cho-Jaehyoung" }, { "family_name": "Grove", "given_name": "Christian A.", "orcid": "0000-0001-9076-6015", "clpid": "Grove-Christian-A" }, { "family_name": "Van Auken", "given_name": "Kimberly", "orcid": "0000-0002-1706-4196", "clpid": "Van-Auken-Kimberly" }, { "family_name": "Chan", "given_name": "Juancarlos", "orcid": "0000-0002-7259-8107", "clpid": "Chan-Juancarlos" }, { "family_name": "Gao", "given_name": "Sibyl", "clpid": "Gao-Sibyl" }, { "family_name": "Sternberg", "given_name": "Paul W.", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" } ], "abstract": "Protein interaction is an important data type to understand the biological function of proteins involved in the interaction, and helps researchers to deduce the biological nature of unknown proteins from the well-characterized functions of their interaction partners. High-throughput studies, coupled with the aggregation of individual experiments, provides a global 'snapshot' of the protein interactions occurring at all levels of biological processes or circumstances. This snapshot of the interaction network, the interactome, is important to understand the overall events up to the level of comparison between species or pathway simulation, or to find new factors yet undefined in the processes, or to add details to the biological processes and pathways. \n\n As of September 2018, WormBase (www.wormbase.org) (Lee et al. 2018) contains 28,279 physical protein-protein interactions for the roundworm Caenorhabditis elegans. Among these, 1500 protein-protein interactions have been curated by BioGRID as a collaboration with WormBase. Within the data set, 17,990 protein-protein interactions are unique, and 6,079 unique genes are involved in these interactions. In order to visualize the overall interaction map, a network diagram for all the unique interactions was generated by using the 'Cytoscape' program, version 3.6.1 (Shannon et al. 2003) (Figure 1A). These numbers represent a 108% increase in the number of interaction annotations since last year, 2017. These interaction data were curated from 1,251 peer-reviewed papers, which were selected from the literature by 'Textpresso Central' using automatic SVM (Support Vector Machine)-based text mining approaches (Fang et al. 2012; M\u00fcller et al. 2018) and manual verification. Compared to other databases providing C. elegans protein-protein interaction, WormBase now presents the largest data set, which has 1.72-fold more interaction annotations than IMEx (Orchard et al. 2012) and 4.51-fold more than BioGRID (Chatr-Aryamontri et al. 2017) (Figure 1B). Most significantly, WormBase now houses the complete protein interaction data from almost all of the C. elegans literature published from 1993 to 2018. The data sets presented at IMEx and BioGRID are annotated from 253 and 174 papers, respectively. All the physical interaction data in WormBase are supported by experimental evidence from original research papers. The statistics of the detection methods used as experimental evidence are shown in Figure 1C. The majority of the interaction data came from high throughput analysis such as large-scale yeast two-hybrid assays or mass-spectrometry, however, a significant portion of the data (13.1%) are supported by more direct detection methods using small-scale, low throughput methods such as co-immunoprecipitation or co-crystallography (Figure 1C). \n\n In WormBase, protein-protein interaction data can be found as a subclass of physical interaction data in the 'Interactions widget' on the gene report page. The Interactions widget provides all types of interaction data related to the gene of interest, such as physical, genetic, regulatory, and predicted interactions. All the interaction data are represented together in a graph created with 'Cytoscape.js' and a table. In the table, the gene names of interaction partners (bait-target) in the interaction are displayed along with the publication. The interaction details including the detection method are also captured in the summary and the remark field in the Interactions page. Users can query the data by using the search bar on the WormBase front page or download all the available data files from the WormBase FTP site (ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/species/c_elegans/PRJNA13758\n/annotation/c_elegans.PRJNA13758.WSXXX.interactions.txt.gz, where WSXXX is the database version release, like \"WS267\"). \n \n All the interaction data in WormBase will be available soon at the new information resource for multiple model organisms, the Alliance of Genome Resources (https://www.alliancegenome.org/). This site will integrate all the interaction data from human and from model organisms C. elegans, budding yeast (Saccharomyces cerevisiae), fruit fly (Drosophila melanogaster), zebrafish (Danio rerio), mouse (Mus musculus) and rat (Rattus norvegicus). Integrated views of interaction data from diverse model organisms will be extremely helpful to build interaction databases for species-to-species comparison, and to establish a disease model quickly based on the database. For the most efficient analysis of the interaction data in WormBase, we are now working on developing a new 'Venn diagram tool' and integrating the 'Gene Set Enrichment Analysis tool' (https://wormbase.org/tools/enrichment/tea/tea.cgi) into the Interactions widget. We will continue to curate other types of macro-molecular interactions including protein-DNA, protein-RNA and RNA-RNA interactions, as well as newly reported protein-protein interaction data to serve our research community.", "doi": "10.17912/micropub.biology.000074", "pmcid": "PMC7255808", "issn": "2578-9430", "publisher": "Caltech Library", "publication": "microPublication Biology", "publication_date": "2018-11-26", "pages": "micropub.biology.000074" }, { "id": "authors:sbxg2-b4p21", "collection": "authors", "collection_id": "sbxg2-b4p21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190321-082336924", "type": "book_section", "title": "Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes", "book_title": "Eukaryotic Genomic Databases", "author": [ { "family_name": "Grove", "given_name": "Christian", "orcid": "0000-0001-9076-6015", "clpid": "Grove-Christian-A" }, { "family_name": "Cain", "given_name": "Scott", "clpid": "Cain-Scott" }, { "family_name": "Chen", "given_name": "Wen J.", "clpid": "Chen-Wen-J" }, { "family_name": "Davis", "given_name": "Paul", "clpid": "Davis-Paul-M" }, { "family_name": "Harris", "given_name": "Todd W.", "orcid": "0000-0003-3406-163X", "clpid": "Harris-Todd-W" }, { "family_name": "Howe", "given_name": "Kevin L.", "clpid": "Howe-Kevin-L" }, { "family_name": "Kishore", "given_name": "Ranjana", "orcid": "0000-0002-1478-7671", "clpid": "Kishore-Ranjana" }, { "family_name": "Lee", "given_name": "Raymond", "orcid": "0000-0002-8151-7479", "clpid": "Lee-Raymond-Y-N" }, { "family_name": "Paulini", "given_name": "Michael", "clpid": "Paulini-Michael-G" }, { "family_name": "Raciti", "given_name": "Daniela", "clpid": "Raciti-Daniela" }, { "family_name": "Tuli", "given_name": "Mary Ann", "clpid": "Tuli-Mary-Ann" }, { "family_name": "Van Auken", "given_name": "Kimberly", "orcid": "0000-0002-1706-4196", "clpid": "Van-Auken-Kimberly-M" }, { "family_name": "Williams", "given_name": "Gary", "clpid": "Williams-Gary-L" }, { "literal": "WormBase Consortium" } ], "contributor": [ { "family_name": "Kollmar", "given_name": "Martin", "clpid": "Kollmar-M" } ], "abstract": "WormBase (www.wormbase.org) provides the nematode research community with a centralized database for information pertaining to nematode genes and genomes. As more nematode genome sequences are becoming available and as richer data sets are published, WormBase strives to maintain updated information, displays, and services to facilitate efficient access to and understanding of the knowledge generated by the published nematode genetics literature. This chapter aims to provide an explanation of how to use basic features of WormBase, new features, and some commonly used tools and data queries. Explanations of the curated data and step-by-step instructions of how to access the data via the WormBase website and available data mining tools are provided.", "doi": "10.1007/978-1-4939-7737-6_14", "pmcid": "PMC6424801", "isbn": "9781493977369", "publisher": "Humana Press", "place_of_publication": "New York, NY", "publication_date": "2018-05-15", "pages": "399-470" }, { "id": "authors:nctet-yw153", "collection": "authors", "collection_id": "nctet-yw153", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171030-085417622", "type": "article", "title": "WormBase 2017: molting into a new stage", "author": [ { "family_name": "Lee", "given_name": "Raymond Y. N.", "orcid": "0000-0002-8151-7479", "clpid": "Lee-Raymond-Y-N" }, { "family_name": "Arnaboldi", "given_name": "Valerio", "orcid": "0000-0002-2563-5374", "clpid": "Arnaboldi-Valerio" }, { "family_name": "Chan", "given_name": "Juancarlos", "orcid": "0000-0002-7259-8107", "clpid": "Chan-Juancarlos" }, { "family_name": "Chen", "given_name": "Wen J.", "clpid": "Chen-Wen-J" }, { "family_name": "Grove", "given_name": "Christian", "orcid": "0000-0001-9076-6015", "clpid": "Grove-Christian-A" }, { "family_name": "Kishore", "given_name": "Ranjana", "orcid": "0000-0002-1478-7671", "clpid": "Kishore-Ranjana" }, { "family_name": "M\u00fcller", "given_name": "Hans-Michael", "clpid": "M\u00fcller-Hans-Michael" }, { "family_name": "Nakamura", "given_name": "Cecilia", "orcid": "0000-0002-4689-7314", "clpid": "Nakamura-Cecilia" }, { "family_name": "Raciti", "given_name": "Daniela", "clpid": "Raciti-Daniela" }, { "family_name": "Schindelman", "given_name": "Gary", "clpid": "Schindelman-Gary" }, { "family_name": "Tuli", "given_name": "Mary Ann", "clpid": "Tuli-Mary-Ann" }, { "family_name": "Van Auken", "given_name": "Kimberly", "orcid": "0000-0002-1706-4196", "clpid": "Van-Auken-Kimberly-M" }, { "family_name": "Wang", "given_name": "Qinghua", "clpid": "Wang-Qinghua" }, { "family_name": "Yook", "given_name": "Karen", "orcid": "0000-0002-4457-6787", "clpid": "Yook-Karen-J" }, { "family_name": "Sternberg", "given_name": "Paul W.", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" } ], "abstract": "WormBase (http://www.wormbase.org) is an important knowledge resource for biomedical researchers worldwide. To accommodate the ever increasing amount and complexity of research data, WormBase continues to advance its practices on data acquisition, curation and retrieval to most effectively deliver comprehensive knowledge about Caenorhabditis elegans, and genomic information about other nematodes and parasitic flatworms. Recent notable enhancements include user-directed submission of data, such as micropublication; genomic data curation and presentation, including additional genomes and JBrowse, respectively; new query tools, such as SimpleMine, Gene Enrichment Analysis; new data displays, such as the Person Lineage browser and the Summary of Ontology-based Annotations. Anticipating more rapid data growth ahead, WormBase continues the process of migrating to a cutting-edge database technology to achieve better stability, scalability, reproducibility and a faster response time. To better serve the broader research community, WormBase, with five other Model Organism Databases and The Gene Ontology project, have begun to collaborate formally as the Alliance of Genome Resources.", "doi": "10.1093/nar/gkx998", "pmcid": "PMC5753391", "issn": "0305-1048", "publisher": "Oxford University Press", "publication": "Nucleic Acids Research", "publication_date": "2018-01-04", "series_number": "D1", "volume": "46", "issue": "D1", "pages": "D869-D874" }, { "id": "authors:h3xnc-tha73", "collection": "authors", "collection_id": "h3xnc-tha73", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151124-111442659", "type": "article", "title": "WormBase 2016: expanding to enable helminth genomic research", "author": [ { "family_name": "Howe", "given_name": "Kevin L.", "clpid": "Howe-Kevin-L" }, { "family_name": "Bolt", "given_name": "Bruce J.", "clpid": "Bolt-Bruce-J" }, { "family_name": "Cain", "given_name": "Scott", "clpid": "Cain-Scott" }, { "family_name": "Chan", "given_name": "Juancarlos", "orcid": "0000-0002-7259-8107", "clpid": "Chan-Juancarlos" }, { "family_name": "Chen", "given_name": "Wen J.", "clpid": "Chen-Wen-J" }, { "family_name": "Davis", "given_name": "Paul", "clpid": "Davis-Paul-M" }, { "family_name": "Done", "given_name": "James", "clpid": "Done-James" }, { "family_name": "Down", "given_name": "Thomas", "clpid": "Down-Thomas" }, { "family_name": "Gao", "given_name": "Sibyl", "clpid": "Gao-Sibyl" }, { "family_name": "Grove", "given_name": "Christian", "orcid": "0000-0001-9076-6015", "clpid": "Grove-Christian-A" }, { "family_name": "Harris", "given_name": "Todd W.", "orcid": "0000-0003-3406-163X", "clpid": "Harris-Todd-W" }, { "family_name": "Kishore", "given_name": "Ranjana", "orcid": "0000-0002-1478-7671", "clpid": "Kishore-Ranjana" }, { "family_name": "Lee", "given_name": "Raymond", "orcid": "0000-0002-8151-7479", "clpid": "Lee-Raymond-Y-N" }, { "family_name": "Lomax", "given_name": "Jane", "clpid": "Lomax-Jane" }, { "family_name": "Li", "given_name": "Yuling", "clpid": "Li-Yuling" }, { "family_name": "Muller", "given_name": "Hans-Michael", "clpid": "M\u00fcller-Hans-Michael" }, { "family_name": "Nakamura", "given_name": "Cecilia", "orcid": "0000-0002-4689-7314", "clpid": "Nakamura-Cecilia" }, { "family_name": "Nuin", "given_name": "Paulo", "clpid": "Nuin-Paul" }, { "family_name": "Paulini", "given_name": "Michael", "clpid": "Paulini-Michael-G" }, { "family_name": "Raciti", "given_name": "Daniela", "clpid": "Raciti-Daniela" }, { "family_name": "Schindelman", "given_name": "Gary", "clpid": "Schindelman-Gary" }, { "family_name": "Stanley", "given_name": "Eleanor", "clpid": "Stanley-Eleanor" }, { "family_name": "Tuli", "given_name": "Mary Ann", "clpid": "Tuli-Mary-Ann" }, { "family_name": "Van Auken", "given_name": "Kimberly", "orcid": "0000-0002-1706-4196", "clpid": "Van-Auken-Kimberly-M" }, { "family_name": "Wang", "given_name": "Daniel", "clpid": "Wang-Daniel-L" }, { "family_name": "Wang", "given_name": "Xiaodong", "clpid": "Wang-Xiaodong" }, { "family_name": "Williams", "given_name": "Gary", "clpid": "Williams-Gary-L" }, { "family_name": "Wright", "given_name": "Adam", "clpid": "Wright-Adam" }, { "family_name": "Yook", "given_name": "Karen", "orcid": "0000-0002-4457-6787", "clpid": "Yook-Karen-J" }, { "family_name": "Berriman", "given_name": "Matthew", "orcid": "0000-0002-9581-0377", "clpid": "Berriman-Matthew" }, { "family_name": "Kersey", "given_name": "Paul", "clpid": "Kersey-Paul" }, { "family_name": "Schedl", "given_name": "Tim", "clpid": "Schedl-Tim" }, { "family_name": "Stein", "given_name": "Lincoln D.", "orcid": "0000-0002-1983-4588", "clpid": "Stein-Lincoln-D" }, { "family_name": "Sternberg", "given_name": "Paul W.", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" } ], "abstract": "WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic species that threaten plant, animal and human health. Research activity using C. elegans as a model system is as vibrant as ever, and we have created new tools for community curation in response to the ever-increasing volume and complexity of data. To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations. Finally, we have developed a new portal for parasitic worm genomes. WormBase ParaSite (parasite.wormbase.org) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research.", "doi": "10.1093/nar/gkv1217", "pmcid": "PMC4702863", "issn": "0305-1048", "publisher": "Oxford University Press", "publication": "Nucleic Acids Research", "publication_date": "2016-01-04", "series_number": "D1", "volume": "44", "issue": "D1", "pages": "D774-D780" } ]