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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PhyloPythiaS Resource Report Resource Website 10+ mentions |
PhyloPythiaS (RRID:SCR_011923) | PPS | analysis service resource, data analysis service, production service resource, service resource | Web Server for Taxonomic Assignment of Metagenome Sequences that is a fast and accurate sequence composition-based classifier that utilizes the hierarchical relationships between clades. Taxonomic assignments with the web server can be made with a generic model, or with sample-specific models that users can specify and create. Several interactive visualization modes and multiple download formats allow quick and convenient analysis and downstream processing of taxonomic assignments. | metagenome, sequence, taxonomy, classification | is listed by: OMICtools | PMID:22745671 PMID:21358620 |
OMICS_01460 | http://phylopythias.cs.uni-duesseldorf.de/index.php?phase=wait | SCR_011923 | 2026-09-19 12:57:25 | 12 | |||||||
|
University of Pittsburgh, Health Sciences Library System Resource Report Resource Website 10+ mentions |
University of Pittsburgh, Health Sciences Library System (RRID:SCR_011975) | HSLS | data or information resource, database | Database access to information services, educational opportunities, and resources in print and electronic format to faculty, students, and researchers in the schools of the health sciences. | journal, book, video |
is listed by: OMICtools has parent organization: University of Pittsburgh; Pennsylvania; USA |
PMID:17108360 | SCR_011975 | Pitt Health Sciences Library System, Pitt HSLS, Health Sciences Library System | 2026-09-19 12:57:26 | 10 | ||||||||
|
OMA Browser Resource Report Resource Website 10+ mentions |
OMA Browser (RRID:SCR_011978) | OMA | data or information resource, database | A database that identifies orthologs among publicly available, complete genomes. It offers a comprehensive search and numerous display options for 4.7 million proteins from 1000 species. The main features are the orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. | protein |
is listed by: OMICtools is related to: GermOnline has parent organization: ETH Zurich; Zurich; Switzerland |
PMID:21113020 PMID:17545180 |
Creative Commons Attribution-ShareAlike License, 2.5 | OMICS_01690 | SCR_011978 | Orthologous MAtrix | 2026-09-19 12:57:26 | 10 | ||||||
|
gsGator Resource Report Resource Website |
gsGator (RRID:SCR_012035) | gsGator | analysis service resource, data analysis service, production service resource, service resource | A web-based platform for functional interpretation of gene sets with features such as cross-species Gene Set Analysis (GSA), Flexible and Interactive GSA, simultaneous GSA for multiple gene set, and and a fully integrated network viewer for both visualizing GSA results and molecular networks. | linux, windows, gene, orthology, pathway, phenotype, mirna target, molecular network, genomic annotation, function |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Ewha Womans University; Seoul; South Korea |
PMID:24423189 | Free, Public | OMICS_02233 | SCR_012035 | 2026-09-19 12:57:26 | 0 | |||||||
|
OrthoDB Resource Report Resource Website 1000+ mentions |
OrthoDB (RRID:SCR_011980) | data or information resource, database | Database of orthologous protein coding genes across vertebrates, arthropods, fungi, basal metazoans, and bacteria. | Hierarchical catalog, ortholog, protein coding genes, mapping genomics to functional data, FASEB list |
is listed by: OMICtools has parent organization: University of Geneva; Geneva; Switzerland |
Swiss National Foundation | PMID:23180791 | Free, Freely available | OMICS_01692 | http://cegg.unige.ch/orthodb7 | SCR_011980 | OrthoDB: Database of Orthologous Groups, OrthoDB v7, OrthoDB - The Hierarchical Catalog of Orthologs, OrthoDB v10 | 2026-09-19 12:57:26 | 1143 | |||||
|
CoreGenomics Resource Report Resource Website |
CoreGenomics (RRID:SCR_011985) | CoreGenomics | blog, data or information resource, narrative resource | This blog focusses on next-generation sequencing and microarray technologies. | is listed by: OMICtools | OMICS_01713 | SCR_011985 | 2026-09-19 12:57:26 | 0 | ||||||||||
|
Bio-IT World Resource Report Resource Website 1+ mentions |
Bio-IT World (RRID:SCR_011986) | Bio-IT World | blog, data or information resource, narrative resource | A leading source of news on technology and innovation in life sciences IT, informatics, genomics, next-gen, drug discovery, development, and clinical trials. | informatics, computer science, biomedical research, drug discovery, information technology, next-generation technology, big data, personalized medicine | is listed by: OMICtools | OMICS_01727 | SCR_011986 | Bio-ITWorld.com, Bio-ITWorld | 2026-09-19 12:57:26 | 3 | ||||||||
|
WebMGA Resource Report Resource Website 100+ mentions |
WebMGA (RRID:SCR_011951) | WebMGA | analysis service resource, data analysis service, production service resource, service resource | A customizable web server for fast metagenomic analysis. |
is listed by: OMICtools has parent organization: University of California at San Diego; California; USA |
OMICS_01524 | SCR_011951 | 2026-09-19 12:57:25 | 196 | ||||||||||
|
GenoREAD Resource Report Resource Website |
GenoREAD (RRID:SCR_012007) | GenoREAD | analysis service resource, data analysis service, production service resource, service resource | A sequence verification pipeline where users can submit trace files to verify if a clone''s physical sequence matches its reference sequence. | clone, verification, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Virginia Bioinformatics Institute |
PMID:23042248 | Acknowledgement requested | OMICS_01823, biotools:genoread | https://bio.tools/genoread | SCR_012007 | GenoREAD - Sequencing Verification Pipeline | 2026-09-19 12:57:26 | 0 | |||||
|
Genomics of Drug Sensitivity in Cancer Resource Report Resource Website 1000+ mentions |
Genomics of Drug Sensitivity in Cancer (RRID:SCR_011956) | Genomics of Drug Sensitivity in Cancer | data or information resource, database | A genomics database project is an academic research program to identify molecular features of cancers that predict response to anti-cancer drugs. | compound, gene, molecule, drug, FASEB list |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Cancer | Wellcome Trust | OMICS_01581 | SCR_011956 | 2026-09-19 12:57:25 | 2388 | |||||||
|
My Biomedical Informatics Blog Resource Report Resource Website |
My Biomedical Informatics Blog (RRID:SCR_012011) | My Biomedical Informatics Blog | blog, data or information resource, narrative resource | A blog about genetics, genomics, and medical research. | is listed by: OMICtools | OMICS_01832 | SCR_012011 | 2026-09-19 12:57:26 | 0 | ||||||||||
|
Cancer Methylome System Resource Report Resource Website 1+ mentions |
Cancer Methylome System (RRID:SCR_012013) | CMS | data or information resource, database | Datbase and web-based system for visualization and analysis of genome-wide methylation data of human cancers. | gene, methylation, visualization |
is listed by: OMICtools has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA |
Cancer, Normal | NCI | PMID:22035855 | Acknowledgement requested | OMICS_01836 | SCR_012013 | 2026-09-19 12:57:26 | 8 | |||||
|
Histone Systematic Mutation Database Resource Report Resource Website |
Histone Systematic Mutation Database (RRID:SCR_012015) | HistoneHits | data or information resource, database | A database for histone mutations and their phenotypes. | is listed by: OMICtools | PMID:19218532 | OMICS_01839 | SCR_012015 | 2026-09-19 12:57:26 | 0 | |||||||||
|
DBCAT Resource Report Resource Website 10+ mentions |
DBCAT (RRID:SCR_012014) | DBCAT | data or information resource, database | A database of CpG islands and analytical tools for identifying comprehensive methylation profiles in cancer cells. | is listed by: OMICtools | Cancer | PMID:21214365 | OMICS_01837 | SCR_012014 | 2026-09-19 12:57:26 | 48 | ||||||||
|
CRAVAT Resource Report Resource Website 10+ mentions |
CRAVAT (RRID:SCR_012776) | CRAVAT | analysis service resource, data analysis service, production service resource, service resource | A web-based application designed with an easy-to-use interface to facilitate the high-throughput assessment and prioritization of genes and missense alterations important for cancer tumorigenesis. |
is listed by: OMICtools has parent organization: Johns Hopkins University; Maryland; USA |
Cancer | NCI CA 152432; NSF DBI 0845275; NCI 1U01CA180956-01 |
OMICS_00147 | SCR_012776 | cancer-related analysis of variants toolkit | 2026-09-19 12:57:27 | 30 | |||||||
|
APPRIS Resource Report Resource Website 50+ mentions |
APPRIS (RRID:SCR_012019) | APPRIS | data or information resource, database | A database that houses annotations of human splice isoforms. It adds reliable protein structural and functional data and information from cross-species conservation. A visual representation of the annotations for each gene allows users to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, it also selects a single reference sequence for each gene, termed the principal isoform, based on the annotations of structure, function and conservation for each transcript. | isoform, function, annotation, splice, reference sequence, structure, conservation, transcript, FASEB list |
is listed by: OMICtools has parent organization: Spanish National Cancer Research Center |
PMID:23161672 | Free | OMICS_01881 | SCR_012019 | APPRIS - A system for annotating alternative splice isoforms | 2026-09-19 12:57:26 | 97 | ||||||
|
ENA Sequence Search Resource Report Resource Website 1+ mentions |
ENA Sequence Search (RRID:SCR_013170) | ENA Sequence Search | analysis service resource, data analysis service, production service resource, service resource | A nucleotide sequence similiary search tool which is far faster than BLAST for large datasets, with only a marginal loss in search sensitivity. | nucleotide sequencing |
is listed by: OMICtools has parent organization: European Nucleotide Archive (ENA) |
OMICS_00993 | SCR_013170 | 2026-09-19 12:57:28 | 7 | |||||||||
|
Human Transcriptome Database for Alternative Splicing Resource Report Resource Website |
Human Transcriptome Database for Alternative Splicing (RRID:SCR_013305) | H-DBAS | data or information resource, database | A specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. H-DBAS offers unique data and viewer for human Alternative Splicing (AS) analysis. It contains: * Genome-wide representative alternative splicing variants (RASVs) identified from following datasets * H-Inv full-length cDNAs (resource summary): H-Invitational cDNA dataset * H-Inv all transcripts (resource summary): Published human mRNA dataset * Mouse full-length cDNAs (resource summary): Mouse cDNA dataset * RASVs affecting protein functions such as protein motif, GO, subcellular localization signal and transmembrane domain * Conserved RASVs compared with mouse genome and the full-length cDNAs (H-Inv full-length cDNAs only) | alternative splicing, alternative splicing variant, cdna, transcriptome, h-invitational, rna-seq, rna, comparative genomics |
is listed by: OMICtools has parent organization: National Institute of Advanced Industrial Science and Technology |
PMID:19969536 PMID:17130147 |
nif-0000-02935, OMICS_01887 | SCR_013305 | H-DBAS - Human-transcriptome DataBase for Alternative Splicing | 2026-09-19 12:57:29 | 0 | |||||||
|
NGS Expert Blog Resource Report Resource Website |
NGS Expert Blog (RRID:SCR_013218) | NGS Expert Blog | blog, data or information resource, narrative resource | Blog including established profound know-how and proprietary protocols to cover a broad range of applications. | next generation sequencing | is listed by: OMICtools | OMICS_01718 | SCR_013218 | 2026-09-19 12:57:29 | 0 | |||||||||
|
PLAN2L Resource Report Resource Website |
PLAN2L (RRID:SCR_013346) | PLAN2L | data or information resource, database, service resource | A web-based online search system that integrates text mining and information extraction techniques to access systematically information useful for analyzing genetic, cellular and molecular aspects of the plant model organism Arabidopsis thaliana. The system facilitates a more efficient retrieval of information relevant to heterogeneous biological topics, from implications in biological relationships at the level of protein interactions and gene regulation, to sub-cellular locations of gene products and associations to cellular and developmental processes, i.e. cell cycle, flowering, root, leaf and seed development. Beyond single entities, also predefined pairs of entities can be provided as queries for which literature-derived relations together with textual evidences are returned. | text mining, bio-entity relation extraction, literature, information extraction, cell cycle, regulation, protein interaction, cellular location, flowering, leave, root, seed, gene, normalization, interaction, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Spanish National Cancer Research Center |
PMID:19520768 | OMICS_01192, biotools:plan2l | https://bio.tools/plan2l | SCR_013346 | PLAN2L: Plant Annotation to Literature, Plant annotation to literature | 2026-09-19 12:57:29 | 0 |
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