Ontogene v2.0 - Resource

Downloads

Description	URL for download
Functional annotation for genes	http://bio-annotation.cn/Ontogene/downloads/annotation.rar
Term associations based on PubMed	http://bio-annotation.cn/Ontogene/downloads/pubmed.rar

Integrated Resources

Type	Database Name [Reference]	URL for download
Ontology	GO [1]	http://geneontology.org/page/download-ontology
	DO [2]	http://disease-ontology.org/downloads/
	HPO [3]	http://purl.obolibrary.org/obo/hp.obo
Gene description	Entrez Gene [4]	ftp://ftp.ncbi.nih.gov/gene/GeneRIF/Homo_sapiens.gene_info.gz
Gene interaction	RNID v2.0 [5]	http://www.rna-society.org/raid/download.html
Functional annotation of genes	GOA for ncRNA [6]	http://geneontology.org/gene-associations/goa_human_rna.gaf.gz
	GOA for mRNA [7]	http://geneontology.org/gene-associations/goa_human.gaf.gz
	HMDD v3.0 [8]	http://www.cuilab.cn/hmdd
	LncRNADisease [9]	http://www.cuilab.cn/lncrnadisease
	CircR2Disease [10]	http://bioinfo.snnu.edu.cn/CircR2Disease/article/DownLoad.aspx
	DiseaseEnhancer [11]	http://biocc.hrbmu.edu.cn/DiseaseEnhancer/
	OMIM [12]	https://omim.org/downloads/
	HPOA [13]	http://human-phenotype-ontology.github.io/downloads.html
	GeneRIF [14]	ftp://ftp.ncbi.nlm.nih.gov/gene/GeneRIF/
Association between terms	MEDLINE [15]	ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/

Our Sister Projects

Resource Name [Reference]	URL for access
DincRNA [15]	http://bio-annotation.cn:18080/DincRNAClient/
MetSigDis [16]	http://bio-annotation.cn/MetSigDis/
LncRNA2Target v2.0 [17]	http://bio-annotation.cn/lncrna2target/

References

(1) Ashburner, M., et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium, Nature genetics, 25, 25-29.
(2) Schriml, L.M., et al. (2012) Disease Ontology: a backbone for disease semantic integration, Nucleic acids research, 40, D940-946.
(3) Robinson, P.N. and Mundlos, S. (2010) The human phenotype ontology, Clinical genetics, 77, 525-534.
(4) Maglott D , et al. (2011) Entrez gene: Gene-centered information at NCBI, Nucleic Acids Research, 39(Database issue):D52-57.
(5) Yi, Y. et al. (2016) RAID v2.0: an updated resource of RNA-associated interactions across organisms[J]. Nucleic Acids Research, 2017, 45, D115-D118.
(6) TR Consortium. (2016) RNAcentral: a comprehensive database of non-coding RNA sequences, Nucleic Acids Research 45, D128.
(7) Camon, E., et al. (2004) The gene ontology annotation (goa) database: sharing knowledge in uniprot with gene ontology, Nucleic acids research, 32, D262-D266.
(8) Huang, Z., et al. (2019) HMDD v3.0: a database for experimentally supported human microRNA-disease associations, Nucleic acids research, 47, D1013-1017.
(9) Chen, G., et al. (2013) LncRNADisease: a database for long-non-coding RNA-associated diseases, Nucleic acids research, 41, D983-986.
(10) Fan, C., et al. (2018) CircR2Disease: a manually curated database for experimentally supported circular RNAs associated with various diseases, Database : the Journal of Biological Databases and Curation. (DOI: 10.1093/database/bay044)
(11) Zhang G, et al. (2018) DiseaseEnhancer: a resource of human disease-associated enhancer catalog. Nucleic Acids Research, 46(D1):D78-D84.
(12) Amberger, J. et al. (2009) McKusick's Online Mendelian Inheritance in Man (OMIM).[J]. Nucleic Acids Research, 37, 793-6.
(13) Kohler, S., et al. (2014) The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data, Nucleic acids research, 42, D966-974.
(14) Lu, Z., et al. (2006), GeneRIF QUALITY ASSURANCE AS SUMMARY REVISION. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing 2007, 269.
(15) Shashikiran, N.D. (2016), MEDLINE, pubmed, and pubmed central (®): Analogous or dissimilar. Journal of the Indian Society of Pedodontics and Preventive Dentistry, 34, 197-198.
(16) Fenton, S and Williams, M. (2005) Getting to know PubMed: an overview, J AHIMA. 76(3), 60A-60D.
(17) Cheng, L., et al. (2018) DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function[J]. Bioinformatics, 2018.
(18) Cheng, L., et al. (2017) MetSigDis: a manually curated resource for the metabolic signatures of diseases[J]. Briefings in Bioinformatics, 2017.