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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Hunter Genomic Facility Resource Report Resource Website |
Hunter Genomic Facility (RRID:SCR_001983) | access service resource, core facility, service resource | Facility which provides instruments and instrument resources for analyzing DNA, RNA, protein, and radio-labeled substances. | genomics, dna, rna, protein, analysis, core facility |
is listed by: Eagle I has parent organization: Hunter College; New York; USA |
Instruction required, Fee | nlx_156341 | http://hunter-cuny.eagle-i.net/i/00000136-7e34-9f73-949b-425080000000 | SCR_001983 | 2026-09-19 12:58:34 | 0 | ||||||||
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EBI Genomes Resource Report Resource Website 10+ mentions |
EBI Genomes (RRID:SCR_002426) | data or information resource, data set | The EBI genomes pages give access to a large number of complete genomes including bacteria, archaea, viruses, phages, plasmids, viroids and eukaryotes. Methods using whole genome shotgun data are used to gain a large amount of genome coverage for an organism. WGS data for a growing number of organisms are being submitted to DDBJ/EMBL/GenBank. Genome entries have been listed in their appropriate category which may be browsed using the website navigation tool bar on the left. While organelles are all listed in a separate category, any from Eukaryota with chromosome entries are also listed in the Eukaryota page. Within each page, entries are grouped and sorted at the species level with links to the taxonomy page for that species separating each group. Within each species, entries whose source organism has been categorized further are grouped and numbered accordingly. Links are made to: * taxonomy * complete EMBL flatfile * CON files * lists of CON segments * Project * Proteomes pages * FASTA file of Proteins * list of Proteins | eukaryote genome, gene, gene browser, genome, archaea genome, bacteria genome, phage genome, plasmid genome, viroid genome, viruse genome, sequence, protein, nucleotide, complete genome, gold standard | has parent organization: European Bioinformatics Institute | nif-0000-02778 | SCR_002426 | Genomes Pages - At the EBI, ENA Genomes Server | 2026-09-19 12:58:34 | 26 | |||||||||
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Drug Design Data Resource Resource Report Resource Website 1+ mentions |
Drug Design Data Resource (RRID:SCR_000497) | D3R | data or information resource, database, portal | Project portal's database of protein-ligand data sets provided by pharmaceutical partners that provide atomic details of drug mechanisms that will be used to improve computer-aided drug-design methods and thus accelerate drug discovery. The project aims to help companies release the high-quality data they have generated, which has incredible value to researchers working to improve methods of computer-aided drug discovery. Everyone stands to benefit from the ability to develop new medications more quickly and inexpensively. What computational chemists globally are trying to do is to make faster, more accurate, more predictive programs to speed up the process. Part of their mission is to engage the community in these challenges to test newly developed predictive algorithms. | computer-aided drug design, drug design, pharmaceutical, small molecule, ligand-protein interaction, protein, ligand, drug development, drug, binding, data set, affinity, computation, medicine, compound, structure |
uses: Binding MOAD uses: Protein Data Bank Bind Database is used by: NIF Data Federation is listed by: DataCite has parent organization: University of California at San Diego; California; USA has parent organization: University of California; California; USA |
NIGMS 1U01GM111528 | nlx_158375 | https://api.datacite.org/dois?prefix=10.15782 | SCR_000497 | Drug Design Data (D3R) Resource | 2026-09-19 12:55:48 | 3 | ||||||
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Systematic Platform for Identifying Mutated Proteins (SysPIMP) Resource Report Resource Website 1+ mentions |
Systematic Platform for Identifying Mutated Proteins (SysPIMP) (RRID:SCR_007954) | SysPIMP | data or information resource, database | A database ofhuman disease-related mutated proteins identified by mass-spectrometry (MS). For achieving this goal, we collected human mutated sequences known to be related to diseases till now. After surveying mutated sequence sources: PMD, OMIM, SwissProt polymorphism, HGMD, etc, we found that currently HGMD contains the largest human gene mutation information. However, because, for academic users, HGMD does not provide with whole data download service, we decided to systematically extract and curate mutation information from PMD, OMIM, SwissProt, MSIPI database to form SysPIMP and provide it free for academic users. | human disease, mutation, protein |
has parent organization: Shanghai Jiao Tong University; Shanghai; China has parent organization: Chinese Academy of Sciences; Beijing; China |
nif-0000-03527 | SCR_007954 | Systematic Platform for Identifying Mutated Proteins | 2026-09-19 12:57:13 | 2 | ||||||||
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SYSTERS Resource Report Resource Website 1+ mentions |
SYSTERS (RRID:SCR_007955) | data or information resource, database | SYSTERS is a database of protein sequences grouped into homologous families and superfamilies. The SYSTERS project aims to provide a meaningful partitioning of the whole protein sequence space by a fully automatic procedure. A refined two-step algorithm assigns each protein to a family and a superfamily. The sequence data underlying SYSTERS release 4 now comprise several protein sequence databases derived from completely sequenced genomes (ENSEMBL, TAIR, SGD and GeneDB), in addition to the comprehensive Swiss-Prot/TrEMBL databases. To augment the automatically derived results, information from external databases like Pfam and Gene Ontology are added to the web server. Furthermore, users can retrieve pre-processed analyses of families like multiple alignments and phylogenetic trees. New query options comprise a batch retrieval tool for functional inference about families based on automatic keyword extraction from sequence annotations. A new access point, PhyloMatrix, allows the retrieval of phylogenetic profiles of SYSTERS families across organisms with completely sequenced genomes. Gene, Human, Vertebrate, Genome, Human ORFs | family, gene, genome, human, human orfs, protein, superfamily, vertebrate | has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany | nif-0000-03528 | SCR_007955 | SYSTERS | 2026-09-19 12:57:13 | 7 | |||||||||
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SUPERFAMILY Resource Report Resource Website 100+ mentions |
SUPERFAMILY (RRID:SCR_007952) | data or information resource, database | SUPERFAMILY is a database of structural and functional protein annotations for all completely sequenced organisms. The SUPERFAMILY annotation is based on a collection of hidden Markov models, which represent structural protein domains at the SCOP superfamily level. A superfamily groups together domains which have an evolutionary relationship. The annotation is produced by scanning protein sequences from over 1,700 completely sequenced genomes against the hidden Markov models. | protein, hmm, hidden markov model, genome, structure, homology, model, FASEB list |
is listed by: 3DVC is related to: DBD: Transcription factor prediction database has parent organization: University of Bristol; Bristol; United Kingdom |
PMID:11697912 | nif-0000-03511 | http://supfam.org, http://stash.mrc-lmb.cam.ac.uk/SUPERFAMILY | SCR_007952 | Superfamily - HMM library and genome assignments server | 2026-09-19 12:57:13 | 345 | |||||||
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Search Tool for Interactions of Chemicals Resource Report Resource Website 1000+ mentions |
Search Tool for Interactions of Chemicals (RRID:SCR_007947) | STITCH | data or information resource, database | Database to explore known and predicted interactions of chemicals and proteins. It integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. The database contains interaction information for over 68,000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database. | drug-target relationship, chemical, chemical-protein interaction, chemical relationship, crystal structure, metabolic pathway interaction, protein, interaction, small molecule, drug, interaction network, FASEB list |
is listed by: OMICtools is related to: Integrated Molecular Interaction Database has parent organization: European Molecular Biology Laboratory |
BMBF ; European Union FP6 EMBO ; ProBioC |
PMID:22075997 PMID:19897548 PMID:18084021 |
r3d100012165, OMICS_01589, nif-0000-03499 | https://doi.org/10.17616/R3606X, https://doi.org/10.17616/R3606X | SCR_007947 | STITCH: Chemical-Protein Interactions | 2026-09-19 12:57:13 | 1054 | |||||
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Topology Data Bank of Transmembrane Proteins Resource Report Resource Website 1+ mentions |
Topology Data Bank of Transmembrane Proteins (RRID:SCR_007964) | TOPDB | data or information resource, database | Collection of transmembrane protein datasets containing experimentally derived topology information from the literature and from public databases. Web interface of TOPDB includes tools for searching, relational querying and data browsing, visualisation tools for topology data. | collection, transmembrane, protein, dataset, topology, public, data, sequence, database |
has parent organization: Hungarian Academy of Sciences; Budapest; Hungary works with: CCTOP |
Bolyai János Scholarship ; Hungarian research and development funds ; OTKA ; Öveges fellowship |
PMID:17921502 | Free, Available for download, Freely available for non commercial users | nif-0000-03568 | SCR_007964 | Topology Data Bank of Transmembrane Proteins, TOPDB | 2026-09-19 12:57:13 | 6 | |||||
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SIMAP Resource Report Resource Website 10+ mentions |
SIMAP (RRID:SCR_007927) | SIMAP | data or information resource, database | It provides a database based on a pre-computed similarity matrix covering the similarity space formed by >4 million amino acid sequences from public databases and completely sequenced genomes. The database is capable of handling very large datasets and is updated incrementally. For sequence similarity searches and pairwise alignments, we implemented a grid-enabled software system, which is based on FASTA heuristics and the Smith Waterman algorithm. SimpleSIMAP and AdvancedSIMAP retrieve homologs for given protein sequences that need to be contained in the SIMAP database. While SimpleSIMAP provides only selected parameters and preconfigured search spaces, the AdvancedSIMAP allows the user to specify search space, filtering and sorting parameters in a flexible manner. Both types of queries result in lists of homologs that are linked in turn to their homologs. So the web interfaces allow users to explore quickly and interactively the protein world by homology. Sponsors: SIMAP is supported by the Department of Genome Oriented Bioinformatics of the Technische Universitt Mnchen and the Institute for Bioinformatics of the GSF-National Research Center for Environment and Health. | genome, alignment, amino acid, homolog, matrix, protein, protein domain and protein classification databases, sequence | SCR_007927 | The Similarity Matrix of Proteins, Similarity Matrix of Proteins | 2026-09-19 12:57:13 | 14 | ||||||||||
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Signaling Pathway Database Resource Report Resource Website 50+ mentions |
Signaling Pathway Database (RRID:SCR_008243) | SPAD | data or information resource, database | It is divided to four categories based on extracellular signal molecules (Growth factor, Cytokine, and Hormone) and stress, that initiate the intracellular signaling pathway. SPAD is compiled in order to describe information on interaction between protein and protein, protein and DNA as well as information on sequences of DNA and proteins. There are multiple signal transduction pathways: cascade of information from plasma membrane to nucleus in response to an extracellular stimulus in living organisms. Extracellular signal molecule binds specific intracellular receptor, and initiates the signaling pathway. Now, there is a large amount of information about the signaling pathway which controls the gene expression and cellular proliferation. We have developed an integrated database SPAD to understand the overview of signaling transduction. | expression, extracellular, gene, cellular, cytokine, dna, growth factor, hormone, intermolecular interactions and signaling pathways databases, intracellular, molecule, organism, pathway, plasma membrane, proliferation, protein, receptor, response, sequence, signal, stimulus, stress, transduction, FASEB list | has parent organization: Kyushu University; Fukuoka; Japan | nif-0000-21376 | SCR_008243 | Signaling Pathway Database | 2026-09-19 12:57:16 | 51 | ||||||||
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Invitrogen iPath Resource Report Resource Website 50+ mentions |
Invitrogen iPath (RRID:SCR_008120) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. LINNEA Pathways is a user-friendly comprehensive online resource for gene- or protein-based scientific research. It is based on a total of 248 signaling and metabolic human biological pathway maps created for Invitrogen by GeneGo. The current version of iPath features 225 maps displaying human regulatory and metabolic pathways established in experimental literature produced by MetaCore from GeneGo, Inc. The map objects (proteins, genes, EC functions, and compounds) are connected via metabolic transformations and physical protein interactions, which were assembled by the GeneGo team of experienced annotators, geneticists, and biochemists. The pathways are organized in a vertical fashion following the general signaling path from signaling molecules and membrane receptors, via signal transduction cascades, to transcription factors and their gene targets. Following the natural organization of cellular machinery with highly interconnected pathways and modules, many maps are linked together via hyperlinked box symbols. Such linkage allows the reconstruction of a big picture view of human cell biology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, metabolic, molecule, pathway, protein, receptor, research, signaling | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20864 | SCR_008120 | iPath | 2026-09-19 12:57:15 | 88 | |||||||||
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Intergrated Transcription Factor Platform Resource Report Resource Website 10+ mentions |
Intergrated Transcription Factor Platform (RRID:SCR_008119) | data or information resource, database | ITFP is an integrated transcription factor (TF) platform, which included abundant TFs and targets message of mammalian. Support vector machine (SVM) algorithm combined with error-correcting output coding (ECOC) algorithm was utilized to identify and classify transcription factor from protein sequence of Human, Mouse and Rat. For transcription factor targets, a reverse engineering method named ARACNE was used to derive potential interaction pairs between transcription factor and downstream regulated gene from Human, Mouse and Rat gene expression profile data. Detailed information of gene expression profile data can be found in help page. Moreover, all data provided by the platform is free for non-commercial users and can be downloaded through links on help page. | expression, gene, human, message, mouse, protein, rat, sequence, target, transcription factor | has parent organization: Fudan University; Shanghai; China | nif-0000-20862 | SCR_008119 | ITFP | 2026-09-19 12:57:14 | 25 | |||||||||
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Interaction Reference Index Web Interface Resource Report Resource Website 10+ mentions |
Interaction Reference Index Web Interface (RRID:SCR_008118) | data or information resource, database | iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from nine different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. Integration is achieved through a rigorously documented procedure for mapping protein IDs across databases, enabling systematic backtracking of the links used to establish the identity of the interaction partners. The iRefWeb interface groups interaction records from the different databases into a single non-redundant view. In particular iRefWeb facilitates comparing interaction records as seen by the various source databases relative to the PubMeds they were annotated from. iRefWeb is one of several views of the iRefIndex resource. Data are also available in a tab-delimited plain-text format (PSI-MITAB) as well as planned releases of a PSI-XML formatted version and a Cytoscape plugin. Further details about the iRefIndex project as well as data downloads are available from here . The method used to build iRefIndex is described in a recent publication. | bind, biogrid, corum, dip, hprd, intact, interaction, mint, mpact, mppi, ophid, protein | nif-0000-20861, r3d100012725 | https://doi.org/10.17616/R31B8K, https://doi.org/10.17616/R31B8K | SCR_008118 | iRefWeb | 2026-09-19 12:57:14 | 27 | |||||||||
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Ingenuity Pathways Knowledge Base Resource Report Resource Website 1000+ mentions |
Ingenuity Pathways Knowledge Base (RRID:SCR_008117) | data or information resource, database | A horizontally and vertically structured database that pulls scientific and medical information and describes it consistently using the Ingenuity Ontology. The Knowledge Base pulls information from journals, public molecular content databases, and textbooks. Data is curated and and integrated into the Knowledge Base . | gene, life science, molecule, protein, research, software, ontology, knowledge base, FASEB list |
is used by: Ingenuity Pathway Analysis is listed by: SoftCite has parent organization: QIAGEN |
Available to the research community, Commercial | nif-0000-20858 | SCR_008117 | Ingenuity Knowledge Base | 2026-09-19 12:57:14 | 4808 | ||||||||
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BoLA Nomenclature: International Society for Animal Genetics Resource Report Resource Website 10+ mentions |
BoLA Nomenclature: International Society for Animal Genetics (RRID:SCR_008142) | data or information resource, database | This website is intended to be the definitive source of information on the bovine major histocompatibility complex - its genes, proteins and polymorphism. Its purpose is to collate data on the Bovine Leucocyte Antigens (BoLA) and provide a forum for the analysis and nomenclature of polymorphisms in the genes and proteins of the bovine MHC. The BoLA nomenclature committee is a standing committee of the International Society for Animal Genetics. Its purpose is to collate data on the Bovine Leucocyte Antigens (BoLA) and provide a forum for the analysis and nomenclature of polymorphisms in the genes and proteins of the bovine MHC. The information gathered here is based on the BoLA workshop reports, which are published in Animal Genetics and the European Journal of Immunogenetics. The workshop report data are reproduced with the permission of the publishers Blackwell Science, and other text on the site is used with the permission of CRC Press. | gene, genetic, animal, antigen, bovine, complex, histocompatibility, immunogenetic, leucocyte, nomenclature, polymorphism, protein, journal article | has parent organization: University of Edinburgh; Scotland; United Kingdom | nif-0000-20967 | http://www.projects.roslin.ac.uk/bola/bolahome.html | SCR_008142 | International Society for Animal Genetics | 2026-09-19 12:57:15 | 16 | ||||||||
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MIPS Mammalian Protein-Protein Interaction Database Resource Report Resource Website 1+ mentions |
MIPS Mammalian Protein-Protein Interaction Database (RRID:SCR_008207) | MIPS, MPPI | data or information resource, database | The MIPS mammalian protein-protein interaction database (MPPI) is a new resource of high-quality experimental protein interaction data in mammals. The content is based on published experimental evidence that has been processed by human expert curators. It is a collection of manually curated high-quality PPI data collected from the scientific literature by expert curators. We took great care to include only data from individually performed experiments since they usually provide the most reliable evidence for physical interactions. To suit different users needs we provide a variety of interfaces to search the database: -Expert interface Simple but powerful boolean query language. -PPI search form Easy to use PPI search -Protein search Just find proteins of interest in the database Sponsors: This work is funded by a grant from the German Federal Ministry of Education and Research. | experimental, human, interaction, intermolecular interactions and signaling pathways databases, mammal, mammalian, pathway, physical, protein |
is related to: Interaction Reference Index is related to: ConsensusPathDB |
nif-0000-21265 | SCR_008207 | The MIPS Mammalian Protein-Protein Interaction Database | 2026-09-19 12:57:16 | 7 | ||||||||
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Mammalian Protein Complex Data Base Resource Report Resource Website |
Mammalian Protein Complex Data Base (RRID:SCR_008209) | data or information resource, database | A database of manually annotated mammalian protein complexes. To obtain a high-quality dataset, information was extracted from individual experiments described in the scientific literature. Data from high-throughput experiments was not included. | gene, genome, mammalian, protein, proteomics, structure | The Munich Information Center for Protein Sequences ; MPCDB |
nif-0000-21273 | SCR_008209 | 2026-09-19 12:57:16 | 0 | ||||||||||
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Migratory Locust EST Database Resource Report Resource Website 1+ mentions |
Migratory Locust EST Database (RRID:SCR_008201) | data or information resource, database | The migratory locust (Locusta migratoria) is an orthopteran pest and a representative member of hemimetabolous insects. Its transcriptomic data provide invaluable information for molecular entomology study of the insect and pave a way for comparative studies of other medically, agronomically, and ecologically relevant insects. This first transcriptomic database of the locust (LocustDB) has been developed, building necessary infrastructures to integrate, organize, and retrieve data that are either currently available or to be acquired in the future. It currently hosts 45,474 high quality EST sequences from the locust, which were assembled into 12,161 unigenes. This database contains original sequence data, including homologous/orthologous sequences, functional annotations, pathway analysis, and codon usage, based on conserved orthologous groups (COG), gene ontology (GO), protein domain (InterPro), and functional pathways (KEGG). It also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. LocustDB also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. It starts with the first transcriptome information for an orthopteran and hemimetabolous insect and will be extended to provide a framework for incorporation of in-coming genomic data of relevant insect groups and a workbench for cross-species comparative studies. | ecologically, entomology, est, fruitfly, functional, gene, agronomically, analysis, annotation, codon, comparative, data, domain, genomic, hemimetabolous, homologous, honeybee, insect, invertebrate, invertebrate databases, locust, locusta migratoria, medically, migratory, molecular, mosquito, nematode, orthologous, orthopteran, pathway, pest, protein, sequence, silkworm, specie, transcriptome, transcriptomic, unigene, ontology | has parent organization: BGI; Shenzhen; China | nif-0000-21244 | SCR_008201 | LocustDB | 2026-09-19 12:57:16 | 7 | |||||||||
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AltSplice Database of Alternative Spliced Events Resource Report Resource Website 1+ mentions |
AltSplice Database of Alternative Spliced Events (RRID:SCR_008162) | data or information resource, database | AltSplice is a computer generated high quality data set of human transcript-confirmed splice patterns, alternative splice events, and the associated annotations. This data is being integrated with other data that is generated by other members of the ASD consortium. The ASD project will provide the following in its three year duration: -human curated database of alternative spliced genes and their properties -a computer generated database of alternatively spliced genes and their properties -the integration of the above and newly found knowledge in a user-friendly interface and research workbench for both bioinformaticists and biologists -DNA chips that are based on the data in the above databases -the DNA chips will be used to test against predisposition for and diagnoses of human diseases ASD aims to analyse this mechanism on a genome-wide scale by creating a database that contains all alternatively spliced exons from human, and other model species. Disease causing mutations seem to induce aberrations in the process of splicing and its regulation. The ASD consortium will develop a DNA microarray (chip) that contains cDNAs of all the splicing regulatory proteins and their isoforms, as well as a chip that contains a number of disease relevant genes. We will concentrate on three models of disease (breast cancer, FTDP-17, male infertility) in which a connection between mis-splicing and a pathological state has been observed. Finally, these chips will be developed as demonstrative kits to detect predisposition for and diagnosis of such diseases. Categories: Nucleotide Sequences: Gene Structure, Introns and Exons, & Splice Sites Databases | event, exon, gene, alternative, annotation, bioinformatic, biology, breast cancer, cdna, chip, diagnosis, disease, dna, human, infertility, intron, isoform, male, microarray, mis-splicing, model, nucleotide, pathological, pattern, property, protein, regulatory, splice, splicing, structure, transcript | has parent organization: European Molecular Biology Laboratory | nif-0000-21021 | SCR_008162 | AltSplice Database of Alternative Spliced Events | 2026-09-19 12:57:15 | 3 | |||||||||
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Database of oligomerization domains from lambda experiments Resource Report Resource Website |
Database of oligomerization domains from lambda experiments (RRID:SCR_008107) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Doodle is a database that was developed to store and distribute information about the protein oligomerization domains that are encoded by various genomes. The protein oligomerization domains described here were found using the lambda repressor fusion system. Doodle uses a schema that is based on EnsEMBL, while also utilizing bioperl modules to both store and retrieve data. The frontend was developed entirely in perl, while the backend utilizes MySQL. GMOD was used to develop the genomic view. | genome, oligomerization, protein | has parent organization: Texas A and M University; Texas; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20834 | SCR_008107 | Doodle | 2026-09-19 12:57:14 | 0 |
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