Updates to the Alliance of Genome Resources central infrastructure

被引：0

作者：

Aleksander, Suzanne A. ^{[1
]}

Anagnostopoulos, Anna V. ^{[2
]}

Antonazzo, Giulia ^{[3
]}

Arnaboldi, Valerio ^{[4
]}

Attrill, Helen ^{[3
]}

Becerra, Andres ^{[5
]}

Bello, Susan M. ^{[2
]}

Blodgett, Olin ^{[2
]}

Bradford, Yvonne M. ^{[6
]}

Bult, Carol J. ^{[2
]}

Cain, Scott ^{[7
]}

Calvi, Brian R. ^{[8
]}

Carbon, Seth ^{[9
]}

Chan, Juancarlos ^{[4
]}

Chen, Wen J. ^{[4
]}

Cherry, J. Michael ^{[1
]}

Cho, Jaehyoung ^{[4
]}

Crosby, Madeline A. ^{[10
]}

De Pons, Jeffrey L. ^{[11
,12
]}

D'Eustachio, Peter ^{[13
]}

Diamantakis, Stavros ^{[5
]}

Dolan, Mary E. ^{[2
]}

dos Santos, Gilberto ^{[10
]}

Dyer, Sarah ^{[5
]}

Ebert, Dustin ^{[14
]}

Engel, Stacia R. ^{[1
]}

Fashena, David ^{[6
]}

Fisher, Malcolm ^{[15
]}

Foley, Saoirse ^{[16
]}

Gibson, Adam C. ^{[11
,12
]}

Gollapally, Varun R. ^{[11
,12
]}

Gramates, L. Sian ^{[10
]}

Grove, Christian A. ^{[4
]}

Hale, Paul ^{[2
]}

Harris, Todd ^{[7
]}

Hayman, G. Thomas ^{[11
,12
]}

Hu, Yanhui ^{[17
]}

James-Zorn, Christina ^{[15
]}

Karimi, Kamran ^{[18
]}

Karra, Kalpana ^{[1
]}

Kishore, Ranjana ^{[4
]}

Kwitek, Anne E. ^{[11
,12
]}

Laulederkind, Stanley J. F. ^{[11
,12
]}

Lee, Raymond ^{[4
]}

Longden, Ian ^{[10
]}

Luypaert, Manuel ^{[5
]}

Markarian, Nicholas ^{[4
]}

Marygold, Steven J. ^{[3
]}

Matthews, Beverley ^{[10
]}

McAndrews, Monica S. ^{[2
]}

机构：

[1] Stanford Univ, Dept Genet, Stanford, CA 94305 USA

[2] Jackson Lab Mammalian Genom, Bar Harbor, ME 04609 USA

[3] Univ Cambridge, Dept Physiol Dev & Neurosci, Downing St, Cambridge CB2 3DY, England

[4] CALTECH, Div Biol & Biol Engn 140 18, Pasadena, CA 91125 USA

[5] European Bioinformat Inst, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England

[6] Univ Oregon, Inst Neurosci, Eugene, OR 97403 USA

[7] Ontario Inst Canc Res, Informat & Biocomp Platform, Toronto, ON M5G 0A3, Canada

[8] Indiana Univ, Dept Biol, Bloomington, IN 47408 USA

[9] Lawrence Berkeley Natl Lab, Environm Genom & Syst Biol, Berkeley, CA USA

[10] Harvard Univ, Biol Labs, 16 Divin Ave, Cambridge, MA 02138 USA

[11] Med Coll Wisconsin, Dept Physiol, Med Coll Wisconsin Rat Genome Database, Milwaukee, WI 53226 USA

[12] Med Coll Wisconsin, Dept Biomed Engn, Med Coll Wisconsin Rat Genome Database, Milwaukee, WI 53226 USA

[13] NYU Grossman Sch Med, New York, NY 10016 USA

[14] Univ Southern Calif, Dept Populat & Publ Hlth Sci, Los Angeles, CA 90033 USA

[15] Cincinnati Childrens Hosp Med Ctr, Div Dev Biol, 3333 Burnet Ave, Cincinnati, OH 45229 USA

[16] Carnegie Mellon Univ, Dept Biol Sci, 5000 Forbes Ave, Pittsburgh, PA 15203 USA

[17] Harvard Med Sch, Howard Hughes Med Inst, Dept Genet, 77 Ave Louis Pasteur, Boston, MA 02115 USA

[18] Univ Calgary, Dept Biol Sci, 507 Campus Dr NW, Calgary, AB T2N 4V8, Canada

来源：

GENETICS | 2024年 / 227卷 / 01期

基金：

英国医学研究理事会;

关键词：

database; knowledgebase; software; text mining; data integration; Drosophila; yeast; Caenorhabditis elegans; zebrafish; mouse; ORTHOLOGY; XENOPUS; SYSTEM;

D O I：

暂无

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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).

引用

页数：18

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