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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Phenoscape Resource Report Resource Website 1+ mentions |
Phenoscape (RRID:SCR_003799) | Phenoscape | data or information resource, portal | Project to create a scalable infrastructure that enables linking phenotypes across different fields of biology by the semantic similarity of their descriptions. | phenotype, bio.tools |
is listed by: Debian is listed by: bio.tools is parent organization of: Teleost Anatomy Ontology is parent organization of: Vertebrate Taxonomy Ontology is parent organization of: Phenoscape Knowledgebase |
NSF DBI-1062404; NSF DBI-1062542; NSF BDI-0641025; NSF EF-0905606; NSF EF-0423641 |
biotools:Phenoscape, nlx_158096 | https://bio.tools/Phenoscape | SCR_003799 | 2026-02-14 02:05:03 | 8 | |||||||
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CATdb: a Complete Arabidopsis Transcriptome database Resource Report Resource Website 10+ mentions |
CATdb: a Complete Arabidopsis Transcriptome database (RRID:SCR_007582) | data or information resource, database | CATdb collects together all the information on transcriptome experiments done at URGV with CATMA micro arrays. All data in CATdb come from the URGV micro array platforms. Common procedures are used including any steps from the experiment design to the statistical analyses. Directed through a WEB interface, biologists enter the standard description of each experimental step (extraction, labelling, hybridization and scanning). Then, normalization and statistical analyses are done following a set of selected methods depending on the experimental design and array types. | catma, microarray, transcriptome, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Evry-Val d'Essonne; Ile-de-France; France |
nif-0000-02639, biotools:catdb | https://bio.tools/catdb | SCR_007582 | CATdb | 2026-02-14 02:06:29 | 40 | ||||||||
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Allele Frequencies in Worldwide Populations Resource Report Resource Website 100+ mentions |
Allele Frequencies in Worldwide Populations (RRID:SCR_007259) | data or information resource, database | The main purpose of the allelefrequencies.net website is to provide one central source, freely available to all. For the storage of allele frequencies from different polymorphic areas in the HUMAN genome. Users can contribute the results of their work into one common database, and can perform database searches on information already available. They have currently collected data in allele, haplotype and genotype format. The success of this website will depend on you to contribute your data. Sponsors: This resource is supported Royal Liverpool University. Keywords: Allele, Polymorphic, Genome, Database, Data, Haplotype, Genotype, | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Royal Liverpool University; Liverpool; United Kingdom |
r3d100011904, biotools:allele_frequency_net, nif-0000-30079 | https://bio.tools/allele_frequency_net https://doi.org/10.17616/R3F063 |
SCR_007259 | Allele Frequencies | 2026-02-14 02:06:03 | 411 | ||||||||
|
Full-Length cDNA Database Resource Report Resource Website 1+ mentions |
Full-Length cDNA Database (RRID:SCR_007666) | data or information resource, database | Full-Length cDNA Database is a resource for cDNA libraries of arhtropods and parasites. The arthropod species covered are Anopheles stephensi, Glossina morsitans (Tsetse fly), and Dermatophagoides farinae (House dust mite), while the parasitic species included are Plasmodium falciparum (Malaria), Toxoplasma gondii, Cryptosporidium parvum, Babesia bovis (Babesia), and Echinococcus multilocularis. A specialized database of each species is available as a link from the home page. This database has been constructed and maintained since 2001 by a Grant-in-Aid for Publication of Scientific Research Results from the Japan Society for the Promotion of Science. Anopheles stephensi, Glossina morsitans, Tsetse fly, Dermatophagoides farinae, House dust mite, Plasmodium falciparum, Malaria, Toxoplasma gondii, Cryptosporidium parvum, Babesia bovis, Babesia, Echinococcus multilocularis, cDNA, cDNA library, arthropod genome, parasite genome | echinococcus multilocularis, anopheles stephensi, arthropod genome, babesia, babesia bovis, cdna, cdna library, cryptosporidium parvum, dermatophagoides farinae, glossina morsitans, house dust mite, malaria, parasite genome, plasmodium falciparum, toxoplasma gondii, tsetse fly, bio.tools |
is listed by: bio.tools is listed by: Debian |
biotools:full-parasites, nif-0000-02856 | https://bio.tools/full-parasites | SCR_007666 | Full-Length cDNA Database | 2026-02-14 02:06:37 | 6 | ||||||||
|
miROrtho: the catalogue of animal microRNA genes Resource Report Resource Website 1+ mentions |
miROrtho: the catalogue of animal microRNA genes (RRID:SCR_007797) | data or information resource, database | It contains predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline. The current release of miROrtho covers 46 animal genomes. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline. | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Geneva; Geneva; Switzerland |
nif-0000-03139, biotools:mirortho | https://bio.tools/mirortho | SCR_007797 | miROrtho | 2026-02-14 02:06:08 | 4 | ||||||||
|
Noncoding RNA database Resource Report Resource Website 10+ mentions |
Noncoding RNA database (RRID:SCR_007815) | ncRNA | data or information resource, database | It is intended to provide information on the sequences and functions of transcripts which do not code for proteins, but perform regulatory roles in the cell. Currently, the database includes over 30,000 individual sequences from 99 species of Bacteria, Archaea and Eukaryota. The primary source of sequences included in the database was the GenBank. Additional annotation information for mouse and human ncRNAs was derived from FANTOM3 database and H-inviational Integrated Database of Annotated Human Genes version 3.4, respectively. Genome mapping information was derived from tha data available at the UCSC Genome Browser site. The sequences and annotations of small cytoplasmic RNAs from bacteria, for which annotation is lacking in the genome sequences, were derived from the Rfam database. The microRNAs or snoRNAs which were available in previous editions, as well as other housekeeping (infrastructural) RNAs (e.g. rRNA, tRNA, snRNA, SRP RNA) are not included in our database to avoid redundancy with more specialized databases which emerged in recent years. | bio.tools |
is listed by: bio.tools is listed by: Debian |
nif-0000-03183, biotools:ncrna | https://bio.tools/ncrna | SCR_007815 | Noncoding RNA database | 2026-02-14 02:06:31 | 13 | |||||||
|
IMG Resource Report Resource Website 500+ mentions |
IMG (RRID:SCR_007733) | IMG | data or information resource, database | Datasets and tools for comparative analysis and annotation of all publicly available genomes from three domains of life in a uniquely integrated context. Plasmids that are not part of a specific microbial genome sequencing project and phage genomes are also included in order to increase its genomic context for comparative analysis. The user interface (see User Interface Map) allows navigating the microbial genome data space along its three key dimensions (genes, genomes, and functions), and groups together the main comparative analysis tools. Microbial genome data analysis in IMG usually starts with the definition of an analysis context in terms of selected genomes, functional annotations, and/or genes, followed by the individual or comparative analysis of genomes, functional annotations, or genes. | genome, microorganism, annotation, bio.tools, FASEB list |
is listed by: 3DVC is listed by: bio.tools is listed by: Debian has parent organization: DOE Joint Genome Institute |
nif-0000-03009, biotools:img | https://bio.tools/img | SCR_007733 | Integrated Microbial Genomes | 2026-02-14 02:06:02 | 652 | |||||||
|
MetaCyc Resource Report Resource Website 1000+ mentions |
MetaCyc (RRID:SCR_007778) | MetaCyc | data or information resource, database | MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 1,200 pathways from more than 1,600 different organisms, and is curated from the scientific experimental literature. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated compounds, enzymes, and genes. | bio.tools, FASEB list |
uses: Pathway Tools is listed by: BioCyc is listed by: bio.tools is listed by: Debian is related to: BioCyc is related to: ENZYME is related to: NCBI BioSystems Database is related to: Algal Functional Annotation Tool is related to: Pathway Tools has parent organization: Stanford Research Institute International works with: MiMeDB |
r3d100011294, nif-0000-03114, biotools:metacyc | https://bio.tools/metacyc https://doi.org/10.17616/R32K7X |
SCR_007778 | 2026-02-14 02:06:31 | 1761 | ||||||||
|
MEROPS Resource Report Resource Website 500+ mentions |
MEROPS (RRID:SCR_007777) | MEROPS, MEROPS fam | data or information resource, database | An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. The MEROPS database uses an hierarchical, structure-based classification of the peptidases. In this, each peptidase is assigned to a Family on the basis of statistically significant similarities in amino acid sequence, and families that are thought to be homologous are grouped together in a Clan. There is a Summary page for each family and clan, and these have indexes. Each of the Summary pages offers links to supplementary pages. About 3000 individual peptidases and inhibitors are included in the database, and there is a Summary page describing each one. You can navigate to this by any of several routes. There are indexes of Name, MEROPS Identifier and source Organism on the menu bar. Each Summary page describes the classification and nomenclature of the peptidase or inhibitor, and provides links to supplementary pages showing sequence identifiers, the structure if known, literature references and more. | peptidase, protease, proteinase, proteolytic enzyme, protein, inhibitor, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: TopFIND has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust WT077044/Z/05/Z | PMID:19892822 | biotools:merops, r3d100012783, nif-0000-03112 | https://bio.tools/merops https://doi.org/10.17616/R33225 https://doi.org/10.17616/R33225 |
SCR_007777 | MEROPS- the Peptidase Database, MEROPS - the Peptidase Database, MEROPS database, MEROPS fam | 2026-02-14 02:06:03 | 736 | |||||
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LOCATE: subcellular localization database Resource Report Resource Website 50+ mentions |
LOCATE: subcellular localization database (RRID:SCR_007763) | data or information resource, database | LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set. The membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing peer-reviewed publications. | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Queensland; Brisbane; Australia |
nif-0000-03086, biotools:locate | https://bio.tools/locate | SCR_007763 | LOCATE | 2026-02-14 02:06:38 | 66 | ||||||||
|
PhyloPat Resource Report Resource Website 1+ mentions |
PhyloPat (RRID:SCR_007851) | data or information resource, database | A database of phylogenetic patterns of evolution between 46 different species. PhyloPat uses the latest release of EnsMart (release 52), and their one-to-one, one-to-many and many-to-many orthologies. First, we stored all of the Ensembl IDs within the 46 species, and the orthologies between them. Second, we determined the evolutionary order of the studied species using the NCBI Taxonomy database. The phylogenetic tree of these species can be viewed here. Third, we used this phylogenetic tree as a starting point for building our phylogenetic lineages. For each gene in the first species (S. cerevisiae), we looked for orthologs in the other species. All orthologs were added to the phylogenetic lineage, and in the next round were checked for orthologs themselves, until no more orthologies were found for any of the genes. This process was repeated for all genes in all species that were not connected to any phylogenetic lineage yet. The complete phylogenetic lineage determination generated 329,998 phylogenetic lineages, consisting of 973,821 genes. These lineages can be queried here by phylogenetic patterns, MySQL regular expressions or simply a list of Ensembl/EMBL/EntrezGene/HGNC IDs. Output can be given in HTML, Excel or plain text format. | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Radboud University; Nijmegen; The Netherlands |
nif-0000-03282, biotools:phylopat | https://bio.tools/phylopat | SCR_007851 | PhyloPat | 2026-02-14 02:06:04 | 2 | ||||||||
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PhylomeDB Resource Report Resource Website 50+ mentions |
PhylomeDB (RRID:SCR_007850) | data or information resource, database | Database for phylomes, that is, complete collections of phylogenetic trees for all proteins encoded in a given genome. It aims at providing a repository of high-quality phylogenies and alignments for proteins encoded in model species. To derive a phylome, each protein encoded in a given genome is used as a seed to retrieve its homologs in other complete genomes. These sequences are aligned and processed to derive reliable phylogenies using several phylogenetic methods. Besides providing the evolutionary history of the gene families, phylomeDB includes phylogeny based predictions of orthology and paralogy relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Genome-wide collections, gene phylogenies, phylogenetic trees collection, proteins encoded, genome, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
PMID:17962297 PMID:21075798 PMID:24275491 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03281, biotools:PhylomeDb | https://bio.tools/PhylomeDB | SCR_007850 | PhylomeDB | 2026-02-14 02:06:39 | 52 | ||||||
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PartiGeneDB Resource Report Resource Website 1+ mentions |
PartiGeneDB (RRID:SCR_007848) | data or information resource, database | A publicly available database resource containing the assembled partial genomes for ~700 eukaryotic organisms. Partial genomes are generated from expressed sequence tag datasets containing more than 1000 sequences. PartiGeneDB allows users to view sets of genes and identify genes of interest in organisms for which a full genome is not currently available. PartiGeneDB is automatically updated to include new organism datasets as they are generated. PartiGeneDB provides four portals of entry into the database. It is hosted and supported by the Hospital for Sick Children, Toronto. In addition to providing a comprehensive resource facilitating comparative analyses, PartiGeneDB allows researchers to access the partial genomes of organisms that may not be available elsewhere. However, we recommend and encourage users interested in exploring datasets from a single organism in more depth, that you visit the specific web sites associated with the sequencing effort associated with that organism . | est, eukaryotic genome, expressed sequence tag, partial genome, bio.tools |
is listed by: bio.tools is listed by: Debian |
nif-0000-03244, biotools:partigenedb | https://bio.tools/partigenedb | SCR_007848 | PartiGeneDB | 2026-02-14 02:06:32 | 6 | ||||||||
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TDR Targets Database Resource Report Resource Website 10+ mentions |
TDR Targets Database (RRID:SCR_007963) | data or information resource, database | This database functions both as a website where researchers can look for information on their targets of interest; and as a tool for prioritization of targets in whole genomes. Using the database as a tool, researchers can quickly prioritize a genome of interest by performing any number of individual queries on a species of interest, then assigning numerical weights to each query (in the history page) to finally obtain a ranked list of genes by combining the weighted queries. This site is part of a WHO/TDR project seeking to exploit the availability of diverse datasets to facilitate the identification and prioritization of drug targets in pathogens causing neglected diseases. | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
nif-0000-03542, biotools:tdr_targets | https://bio.tools/tdr_targets | SCR_007963 | TDR Targets | 2026-02-14 02:06:06 | 43 | ||||||||
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RNA Virus Database Resource Report Resource Website |
RNA Virus Database (RRID:SCR_007899) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. It is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments (in species where more than one isolate has been fully sequenced) and contains translated genome sequences for all species. It has been created for two main purposes: to facilitate the comparative analysis of RNA viruses and to become a hub for other, more specialised virus Web sites. | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Oxford; Oxford; United Kingdom |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:rnavirusdb | https://bio.tools/rnavirusdb | http://virus.zoo.ox.ac.uk/rnavirusdb/ | SCR_007899 | RNA Virus Database | 2026-02-14 02:06:32 | 0 | ||||||
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Phospho.ELM Resource Report Resource Website 10+ mentions |
Phospho.ELM (RRID:SCR_001109) | data or information resource, database | Database of experimentally verified phosphorylation sites in eukaryotic proteins. Entries are manually curated with links to literature references, information about structure, interaction partners and sub-cellular compartment tissues, and sequences from the UniProt database. | eukaryotic protein, phosphorylation site, database, curation, bio.tools, FASEB list |
uses: UniProt is listed by: bio.tools is listed by: Debian has parent organization: University of Dundee; Scotland; United Kingdom |
PMID:17962309 | Publicly available | nif-0000-03278, biotools:phosphoelm | https://bio.tools/phosphoelm | SCR_001109 | 2026-02-14 02:05:44 | 40 | |||||||
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iontree Resource Report Resource Website |
iontree (RRID:SCR_002813) | software resource | Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24958264 | Free, Freely available, Available for download | OMICS_02656, biotools:iontree | https://bio.tools/iontree | SCR_002813 | iontree: Data management and analysis of ion trees from ion-trap mass spectrometry | 2026-02-14 02:04:50 | 0 | ||||||
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HSSP Resource Report Resource Website 10+ mentions |
HSSP (RRID:SCR_004953) | HSSP | data or information resource, database | HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein. Homologues are very likely to have the same 3D structure as the PDB protein to which they have been aligned. As a result, the database is not only a database of sequence aligned sequence families, but it is also a database of implied secondary and tertiary structures. Likely secondary structure are carried over from the PDB protein to each homologous protein. Tertiary structure models can be built by fitting the sequence of the homologue as aligned into the 3D template of the protein of known structure. Special software is needed to construct 3D models by homology, such WHATIF by Gert Vriend or MaxSprout by Liisa Holm and Chris Sander. The command rsync can be used to obtain a local copy of the HSSP. We appreciate receiving an Email from people who do so, but there are no strings attached. Everybody can freely download the files, academia and industry alike. If your institute''s firewall doesn''t allow you to use the (preferred) rsync way of obtaining HSSP files, feel free to work with FTP. The files are in that case available from: ftp://ftp.cmbi.ru.nl//pub/molbio/data/hssp/ | gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Radboud University; Nijmegen; The Netherlands |
PMID:2017436 | biotools:hssp, nlx_91976 | https://bio.tools/hssp | SCR_004953 | Homology-derived Secondary Structure of Proteins, homology-derived structures of proteins, HSSP - Homology derived Secondary Structure of Proteins, HSSP database, HSSP - Homology-derived Secondary Structure of Proteins, Homology derived Secondary Structure of Proteins | 2026-02-14 02:06:23 | 33 | ||||||
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STING Report Resource Report Resource Website 1+ mentions |
STING Report (RRID:SCR_005121) | STING | data or information resource, database | Sting Report is a database of amino acid sequences, structures, functions, and parameters. It allows users to easily extract from the Blue Star Sting Database detailed but focused information about an individual amino acid, which belongs to a structure described in a PDB file. The extracted information is presented as a series of GIF images and a table, which are generated by Blue Star Sting modules and contain values of up to 125 sequence/structure/function descriptors/parameters. The HTML page resulting from a query on Sting Report, containing the GIF images and the table, is printable, and can also be composed and visualized at a computer platform with elementary configuration. | amino acid, amino acid function, amino acid sequence, amino acid structure, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:15608194 | nif-0000-03498, biotools:sting_millenium | https://bio.tools/sting_millenium | SCR_005121 | Blue Star Sting Report | 2026-02-14 02:06:25 | 4 | ||||||
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Apo and Holo structures DataBase Resource Report Resource Website 1+ mentions |
Apo and Holo structures DataBase (RRID:SCR_004800) | AH-DB | data or information resource, database | Database of apo and holo structure pairs of proteins before and after binding. Various protein functions have been shown directly associated with conformational transitions triggered by binding other molecules. Tertiary structures determined in the unbound and bound state are usually named apo and holo structures, respectively. AH-DB is the largest database of apo-holo structure pairs and provides a sophisticated interface to search and view the collected data. It contains 746314 apo-holo pairs of 3638 proteins from 702 organisms. | ah-db, ahdb, apo, holo, protein interaction, structural change, protein, protein structure, protein binding, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: National Cheng Kung University; Tainan; Taiwan |
National Science Council Taiwan NSC 99-2628-E-006-017 | PMID:22084200 | The community can contribute to this resource | biotools:ah-db, nlx_143908 | https://bio.tools/ah-db | SCR_004800 | Apo-Holo DataBase | 2026-02-14 02:06:20 | 1 |
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