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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Malaria Parasite Metabolic Pathways
 
Resource Report
Resource Website
10+ mentions
Malaria Parasite Metabolic Pathways (RRID:SCR_007072) Malaria Parasite Metabolic Pathways data set, data or information resource, image collection Data set of metabolic pathways for the malaria parasite based on the present knowledge of parasite biochemistry and on pathways known to occur in other unicellular eukaryotes. This site extracted the pertinent information from the universal sites and presented them in an educative and informative format. The site also includes, cell-cell interactions (cytoadherence and rosetting), invasion of the erythrocyte by the parasite and transport functions. It also contains an artistic impression of the ultrastructural morphology of the interaerythrocytic cycle stages and some details about the morphology of mitochondria and the apicoplast. Most pathways are relevant to the erythrocytic phase of the parasite cycle. All maps were checked for the presence of enzyme-coding genes as they are officially annotated in the Plasmodium genome (http://plasmodb.org/). The site is constructed in a hierarchical pattern that permits logical deepening: * Grouped pathways of major chemical components or biological process ** Specific pathways or specific process *** Chemical structures of substrates and products or process **** Names of enzymes and their genes or components of process Each map is linked to other maps thus enabling to verify the origin of a substrate or the fate of a product. Clicking on the EC number that appears next to each enzyme, connects the site to BRENDA, SWISSPROT ExPASy ENZYME, PlasmoDB and to IUBMB reaction scheme. Clicking of the name of a metabolite, connects the site to KEGG thus providing its chemical structure and formula. Next to each enzyme there is a pie that depicts the stage-dependent transcription of the enzyme''s coding gene. The pie is constructed as a clock of the 48 hours of the parasite cycle, where red signifies over-transcription and green, under-transcription. Clicking on the pie links to the DeRisi/UCSF transcriptome database. enzyme, gene, genome, map, metabolic, mosquito, parasite, pathway, plasmodium falciparum, protein, reaction, sequence, metabolic pathway, chemical structure, cell-cell interaction, transport, morphology, mitochondria, apicoplast has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel Malaria UNDP/World Bank/WHO Special Programme ;
NIAID ;
European Union ;
6th FP- BioMalPar Network of Excellence on Biology and Pathology of the Malaria Parasite
nif-0000-21249 SCR_007072 2026-02-16 09:46:52 20
BioMANTA
 
Resource Report
Resource Website
1+ mentions
BioMANTA (RRID:SCR_007177) BioMANTA controlled vocabulary, research forum portal, software resource, topical portal, portal, ontology, data or information resource, disease-related portal This project encompasses development of novel biological network analysis methods and infrastructure for querying biological data in a semantically-enabled format, and aims to create a semantic interactome model. Research within the BioMANTA project will focus on computational modelling and analysis, primarily using Semantic Web technologies and Machine Learning methods, of large-scale protein-protein interaction and compound activity networks across a wide variety of species. A range of information such as kinetic activity, tissue expression, and subcellular localization and disease state attributes will be included in the resulting data model. Protein interactions are a fundamental component of biological processes. Many proteins are functional only in multimeric complexes, or require interaction partners to achieve their correct localisation or function. For this reason, the study of protein-protein interaction (PPI) networks has become an area of growing interest in computational biology. Through the use of Semantic Web technologies such as Resource Description Framework (RDF) and Web Ontology Language (OWL), interaction data is modelled to create a knowledge representation in which meaning is vested in the ontology rather than instances of data. Stochastic and computational intelligence methods are applied to this data to infer high coverage networks. Semantic inferencing is used to infer previously unknown and meaningful pathways. Major project components: - The BioMANTA Ontology:- An OWL DL ontology incorporating the PSI-MI Ontology, the NCBI Taxonomy, and elements of BioPax ontology and Gene Ontology (describing subcellular localisation). This allows us to re-use existing ontologies, thereby reducing overheads associated with knowledge acquisition in the ontology development process. We are able to integrate existing public data that contain annotation in these formats. - Data conversion & semantic protein integration:- A set of software components that convert protein-protein databases (DIP, MPact, IntAct, etc.) from PSI-MI XML to RDF compliant with the BioMANTA ontology. These software allow us to make these protein-protein interaction datasets (and more generally, any PSI-MI XML data) semantically available for querying and inference within BioMANTA. - A RDF triple store based on RDF Molecules and the MapReduce architecture:- A proof-of-concept RDF triple store using RDF molecules and Hadoop scale-out architectures. Regular RDF graphs are deconstructed into RDF molecules, which are distributed over distributed compute nodes in the MapReduce architecture, and are subsequently combined to form equivalent RDF graphs. Such an approach makes the distributed SPARQL querying and reasoning on RDF triple stores possible. - A quantitative framework to integrate networks extracted from independent data sources (gene expression, subcellular localization, and ortholog mapping):- The model is multi-layer, with a first layer based on Decision Trees where each Decision tree is built on each dataset independently. The tree nodes are cut using Shannon''s entropy (mutual information); the decision of these independent trees is integrated using logistic regression, and the parameters are optimised using maximum likelihood. Sponsors: This resource is supported by the Pfizer Global Research and Development, the Institute for Molecular Bioscience (IMB), and the University of Queensland, Australia. biological, network, model, analysis, semantic, interactome, biological, data, development, computational, process, protein, biology, ontology, knowledge, molecule, rdf, framework, subcellular, localization, gene, expression, ortholog, mapping, dataset has parent organization: University of Queensland; Brisbane; Australia nif-0000-30183 SCR_007177 The Modelling and Analysis of Biological Network Activity 2026-02-16 09:46:54 2
Caenorhabditis Genetics Center
 
Resource Report
Resource Website
1000+ mentions
Caenorhabditis Genetics Center (RRID:SCR_007341) CGC organism supplier, material resource, biomaterial supply resource, cell repository Center that acquires, maintains, and distributes genetic stocks and information about stocks of the small free-living nematode Caenorhabditis elegans for use by investigators initiating or continuing research on this genetic model organism. A searchable strain database, general information about C. elegans, and links to key Web sites of use to scientists, including WormBase, WormAtlas, and WormBook are available. non-human animal, caenorhabditis elegans, chromosome, database, model, mutant, nematode, nomenclature, model organism, protein, transgenic, web accessible database, genetic stock, germplasm, genotype, FASEB list is used by: NIF Data Federation
is listed by: One Mind Biospecimen Bank Listing
is related to: C. elegans Gene Knockout Consortium
is related to: Expression Patterns for C. elegans promoter GFP fusions
has parent organization: University of Minnesota Twin Cities; Minnesota; USA
NIH OD010440 nif-0000-00240 https://orip.nih.gov/comparative-medicine/programs/invertebrate-models
http://www.cbs.umn.edu/research/resources/cgc
http://biosci.umn.edu/CGC/, http://www.cgc.cbs.umn.edu SCR_007341 2026-02-16 09:46:56 3842
BioInfoBank Meta Server
 
Resource Report
Resource Website
10+ mentions
BioInfoBank Meta Server (RRID:SCR_007181) BioInfoBank data or information resource, topical portal, portal This service offers a gateway to well-benchmarked protein structure and function prediction methods. Structural models collected from the prediction servers are assessed using the powerful 3D-jury consensus approach. The Structure Prediction Meta Server provides access to various fold recognition, function prediction and local structure prediction methods. The Server takes the amino acid sequence of the query protein, the reference name for the prediction job, and the E-mail address as input. The E-mail address is used only for notification about errors during the execution of the job. The query sequence and the reference name are placed in the process queue. The Meta Server accepts only sequences, which have not been submitted before. In case of duplicate sequences the second user will be notified with a link to the previous submission. Sequences longer than 800 amino acids are not accepted by some services. The internal SQL database offers the possibility to find any previous jobs processed by the Meta Server using regular expressions addressing field like E-mail, Job Name and the host name, from which the job was initiated. Each server has its own process queuing system managed by the Meta Server. All results of fold recognition servers are translated into uniform formats. The information extracted from the raw output of the servers includes the PDB codes of the hits, the alignments and the similarity (reliability) scores specific for every server. Mapping of the hits to the SCOP and FSSP classifications are made either using known PDB representatives or alignment of the template sequence with the databases of proteins in both classifications. The secondary structure assignments for all hits are taken from the mapped FSSP (red for helices and blue for strands). Underscored amino acids indicate the first residue after an insertion in the template sequence. The Meta server provides translation of the alignments in standard formats like FASTA, PDB or CASP. The Meta Server is coupled to consensus servers. They provide jury predictions based on the results collected from other services. Not all fold recognition servers are used by the jury system. The data stored on the meta server is available through http://meta.bioinfo.pl/data/JOBID/. Jobs older than 2 months are not shown. The Meta Server is only a set of programs aimed to process and manage biological data, while the predictive power of the service comes from (mostly) remote prediction providers. Sponsors: This resource is supported by The BioInfoBank Institute. server, meta, biology, function, protein, structure, method, model, prediction, 3-dimentional, amino acid, sequence nif-0000-30180 http://meta.bioinfo.pl SCR_007181 The BioInfoBank Meta Server, BioInfoBank Meta Server 2026-02-16 09:46:54 22
CCP4
 
Resource Report
Resource Website
1000+ mentions
CCP4 (RRID:SCR_007255) CCP4 software application, data processing software, data analysis software, portal, software resource, simulation software, service resource, data or information resource Portal for Macromolecular X-Ray Crystallography to produce and support an integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques. Used in the education and training of scientists in experimental structural biology for determination and analysis of protein structure. macromolecular, x-ray, crystallography, biophysical, technique, structural, biology, analysis, protein, Research Complex at Harwell, computational, collaborative, project is used by: MoRDa
is used by: PDB-REDO
is listed by: SoftCite
is related to: BALBES
is related to: CCP4mg
is related to: fragon
is related to: ConPlot
has parent organization: Science and Technology Facilities Council
Science and Technology Facilities Council Free, Available for download, Freely available, Tutorial available SCR_016709, nif-0000-30238 SCR_007255 The Collaborative Computational Project Number 4 in Protein Crystallography, Collaborative Computational Project Number 4 2026-02-16 09:46:55 4740
Biostrings
 
Resource Report
Resource Website
100+ mentions
Biostrings (RRID:SCR_016949) software application, data processing software, sequence analysis software, data analysis software, software resource Software package for efficient manipulation of biological strings. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. manipulation, biological, string, memory, efficient, container, sequence, set, DNA, RNA, protein is used by: riboWaltz
is listed by: Bioconductor
is related to: R Project for Statistical Computing
has parent organization: Stanford University; Stanford; California
Free, Available for download, Freely available https://web.stanford.edu/class/bios221/labs/biostrings/lab_1_biostrings.html SCR_016949 2026-02-16 09:49:07 167
iDTI-ESBoost
 
Resource Report
Resource Website
iDTI-ESBoost (RRID:SCR_016720) iDTI-ESBoost service resource, software application, software resource, simulation software Software tool for identification of Drug Target Interaction using Evolutionary and Structural features with Boosting. Used to predict drug-protein interactions. identification, drug, target, interaction, evolutionary, structural, feature, boost, predict, protein PMID:29255285 Free, Freely available http://farshidrayhan.pythonanywhere.com/iDTI-ESBoost/ SCR_016720 identification of Drug Target Interaction using Evolutionary and Structural features with Boosting 2026-02-16 09:49:05 0
National Resource for Translational and Developmental Proteomics
 
Resource Report
Resource Website
National Resource for Translational and Developmental Proteomics (RRID:SCR_016907) NRTDP training resource, organization portal, portal, service resource, data or information resource Organization dedicated to analysis of protein molecules by mass spectrometry, with a focus on intact protein measurements. Biomedical projects originated from clinical and basic research programs that utilize both targeted and untargeted analyses. Used for the development of new technology, training and dissemination of proteomics methods to laboratories and scientists. protein, mass, spectrometry, proteomics, measurement, targeted, untargeted, analysis has parent organization: Northwestern University; Illinois; USA
provides: ProSight Lite
NIGMS P41 GM108569 SCR_016907 The National Resource for Translational and Developmental Proteomics, NRTDP 2026-02-16 09:49:07 0
OmicsNet
 
Resource Report
Resource Website
10+ mentions
OmicsNet (RRID:SCR_016724) web service, data access protocol, analysis service resource, software resource, production service resource, service resource Web based tool to create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space (genes/proteins, microRNAs, transcription factors or metabolites). create, molecular, interaction, network, visually, 3D, gene, protein, microRNA, transcription factor, metabolite, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
Natural Sciences and Engineering Research Council of Canada ;
Genome Canada ;
Canada Research Chairs Program
PMID:29878180 Free, Freely available biotools:omicsnet https://bio.tools/omicsnet SCR_016724 2026-02-16 09:49:05 39
Clonotator
 
Resource Report
Resource Website
Clonotator (RRID:SCR_016730) software application, data processing software, web service, sequence analysis software, data analysis software, data access protocol, image analysis software, software resource, alignment software Web based platform that integrates several bioinformatics tools for screening and annotation of cDNA construct sequences. Translates the nucleotide sequence of the construct into an amino acid sequence, aligns the predicted sequence to a reference database of protein sequences and identifies the best protein and isoform match, annotates any variants present in the construct, and incorporates disease-associated mutations and transcriptomic data. screening, annotation, cDNA, sequence, amino acid, align, reference, database, protein, disease, mutation, transcriptomic, data has parent organization: University of California at San Francisco; California; USA Free, Freely available, Registration required https://willseylab.com/clonotator/ SCR_016730 2026-02-16 09:49:05 0
CPTAC
 
Resource Report
Resource Website
100+ mentions
CPTAC (RRID:SCR_017135) organization portal, topical portal, consortium, portal, data or information resource, disease-related portal Clinical proteomic tumor analysis consortium to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, in order to understand molecular basis of cancer that is not possible through genomics and to accelerate translation of molecular findings into clinic. Operates through Proteome Characterization Centers, Proteogenomic Translational Research Centers, and Proteogenomic Data Analysis Centers. CPTAC investigators collaborate, share data and expertise across consortium, and participate in consortium activities like developing standardized workflows for reproducible studies. identify, protein, alteration, cancer, genome, clinical, study, proteome, proteogenomic, tumor, data, analysis, consortium, reproducibility has parent organization: National Cancer Institute cancer SCR_017135 Clinical Proteomic Tumor Analysis Consortium 2026-02-16 09:49:10 131
OmicsSIMLA
 
Resource Report
Resource Website
1+ mentions
OmicsSIMLA (RRID:SCR_017011) software application, software resource, simulation software, software toolkit Software tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version. multi, omics, data, simulator, disease, genomic, epigenomic, transcriptomic, proteomic, genome, sequencing, protein, RNA is listed by: OMICtools Ministry of Science and Technology in Taiwan DOI:10.1101/426510 Freely available, Available to download, Free OMICS_31363 SCR_017011 2026-02-16 09:49:08 1
University of Cambridge Centre for Trophoblast Research Bioinformatics Core Facility
 
Resource Report
Resource Website
University of Cambridge Centre for Trophoblast Research Bioinformatics Core Facility (RRID:SCR_017192) CTR Bioinformatics Core Facility training service resource, core facility, access service resource, data analysis service, analysis service resource, production service resource, service resource Core provides assistance with experimental design, RNA sequencing, whole genome and targeted sequencing, methylation sequencing, protein alignment, microscopy image analysis, and training. bioinformatics, sequencing, RNA, genome, methylation, protein, alignment, data, image, analysis has parent organization: University of Cambridge; Cambridge; United Kingdom Restricted SCR_017192 Center for Trophoblast Research, Centre for Trophoblast Research, Bioinformatics Core Facility, University of Cambridge 2026-02-16 09:49:11 0
Clustal 2
 
Resource Report
Resource Website
1000+ mentions
Clustal 2 (RRID:SCR_017055) software application, data processing software, data visualization software, image analysis software, software resource, alignment software Software tool for nucleotide sequence alignment. Graphical version of multiple sequence alignment program for DNA and proteins. Windows interface for ClustalW multiple sequence alignment program. Provides integrated environment for performing multiple sequence and profile alignments and analyzing results. Available on Linux, Mac and Windows. graphical, multiple, sequence, alignment, DNA, protein is related to: Clustal W2
is related to: Clustal Omega
Science Foundation Ireland ;
INSERM ;
CNRS ;
Ministère de la Recherche et Technologie ;
EMBL
PMID:17846036
PMID:9396791
Free, Available for download, Freely available biotools:clustal2 http://www.clustal.org/download/clustalx_help.html
https://bio.tools/clustal2
SCR_017055 Clustalx, CLUSTAL_X, clustalx, clustal X, clustal2 2026-02-16 09:49:09 1480
GO Gene Ontology Consortium and Knowledgebase
 
Resource Report
Resource Website
1+ mentions
GO Gene Ontology Consortium and Knowledgebase (RRID:SCR_017505) GOC data or information resource, organization portal, consortium, portal Consortium integrates resources from variety of research groups, from model organisms to protein databases to biological research communities actively involved in development and implementation of Gene Ontology. Mission to develop up to date, comprehensive, computational model of biological systems, from molecular level to larger pathways, cellular and organism level systems. Integrate, resource, model, organism, protein, database, gene, ontology, develope, cellular, system NHGRI HG002273;
NHGRI U24 HG012212
SCR_017505 GO Consortium, Gene Ontology Consortium 2026-02-16 09:49:15 8
PathwayNet
 
Resource Report
Resource Website
1+ mentions
PathwayNet (RRID:SCR_017353) web service, data analysis service, analysis service resource, data access protocol, software resource, production service resource, service resource Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks. Interface, interaction, predict, human, gene, network, integrative, analysis, user, data, tissue, cell, functional, protein, genome is listed by: OMICtools
has parent organization: Princeton University; New Jersey; USA
NIGMS R01 GM071966;
NHGRI HG005998;
NIGMS P50 GM071508
PMID:25431329 Free, Freely available SCR_017353 2026-02-16 09:49:13 7
RAMPAGE
 
Resource Report
Resource Website
100+ mentions
RAMPAGE (RRID:SCR_017590) web service, data access protocol, analysis service resource, software resource, production service resource, service resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2021.Web based structural analysis tool for any uploaded PDB file, producing Ramachandran plots, computing dihedral angles and extracting sequence from PDB. Used to visualize dihedral angles ψ against φ of amino acid residues in protein structure. Ramachandran, plot, analysis, upload, PDB, file, coputing, dihedral, angle, extracting, sequence, protein, amino acid, residue, structure has parent organization: University of Cambridge; Cambridge; United Kingdom THIS RESOURCE IS NO LONGER IN SERVICE. SCR_017590 2026-02-16 09:49:16 124
ProtParam Tool
 
Resource Report
Resource Website
5000+ mentions
ProtParam Tool (RRID:SCR_018087) software application, data processing software, sequence analysis software, data analysis software, analysis service resource, software resource, production service resource, service resource Software tool to calculate various physicochemical parameters for given protein stored in Swiss-Prot or TrEMBL or for user entered protein sequence. Protein can either be pecified as Swiss-Prot/TrEMBL accession number or ID, or in form of raw sequence. Computed parameters include molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity. Calculate phycicochemical parameter, protein, Swiss-Prot, TrEMBL, protein sequence, molecular weight, theortical pl, amino acid composition, atomic composition, extinction coefficient, bio.tools is listed by: Debian
is listed by: bio.tools
is related to: ExPASy Bioinformatics Resource Portal
NHGRI U01 HG02712;
Swiss Federal Government through Federal Office of Education and Science
PMID:10027275 Free, Freely available biotools:protparam https://bio.tools/protparam SCR_018087 ProtParam 2026-02-16 09:49:24 5406
MUMmer
 
Resource Report
Resource Website
100+ mentions
MUMmer (RRID:SCR_018171) software application, data processing software, image analysis software, software resource, alignment software Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes. Align, genome, DNA, protein, sequence, , bio.tools is listed by: bio.tools
is listed by: Debian
is listed by: OMICtools
is listed by: SoftCite
is related to: MUMmerGPU
NLM R01 LM06845;
NSF IIS 9902923;
NIAID N01 AI15447
PMID:14759262 Free, Available for download, Freely available OMICS_14554, biotools:mummer https://github.com/mummer4/mummer
https://bio.tools/mummer
https://sources.debian.org/src/mummer/
SCR_018171 MUMmer4, MUMmer 3.0 2026-02-16 09:49:27 480
SARS-CoV-2-Sequences
 
Resource Report
Resource Website
10+ mentions
SARS-CoV-2-Sequences (RRID:SCR_018319) data set, data repository, storage service resource, service resource, data or information resource Collection of SARS-CoV-2 sequences currently available in GenBank genetic sequence database and Sequence Read Archive. Updated as additional sequences are released. SARS-CoV-2, SARS coronavirus, SARS-CoV infection, Coronavirus, data, SARS-CoV-2 sequence collection, nucleotide, genome, Betacoronavirus, protein works with: GenBank
works with: NCBI Sequence Read Archive (SRA)
COVID-19 The Federal Government Free, Available for download, Freely available SCR_018319 Severe Acute Respiratory Syndrome CoronaVirus 2 Sequences 2026-02-16 09:49:28 28

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