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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Human Disease Ontology Resource Report Resource Website 1+ mentions |
Human Disease Ontology (RRID:SCR_000476) | DO | data or information resource, ontology, controlled vocabulary, database | Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases. | obo, pathological, organismal, cellular, disease, biomedical, health, neurologic disease, neurological disorder, phenotype, bio.tools, |
is used by: DOAF is listed by: BioPortal is listed by: OBO is listed by: bio.tools is listed by: Debian is related to: PharmGKB Ontology is related to: GWASdb is related to: NUgene Project is related to: FunDO is related to: Neurocarta has parent organization: University of Maryland School of Medicine; Maryland; USA |
NHGRI U24 HG012557 | PMID:22080554 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-35926, nlx_157432, SCR_003491, biotools:disease_ontology | http://disease-ontology.org/ https://bio.tools/disease_ontology http://purl.obolibrary.org/obo/doid.obo |
http://do-wiki.nubic.northwestern.edu/index.php/Main_Page | SCR_000476 | Human Disease Ontology Knowledgebase, Disease Ontology | 2026-02-14 01:59:45 | 5 | |||
|
Gazetteer Resource Report Resource Website 1+ mentions |
Gazetteer (RRID:SCR_000473) | GAZ | data or information resource, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available. | obo, owl |
is listed by: BioPortal is listed by: OBO has parent organization: Genomic Standards Consortium |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157412 | http://purl.obolibrary.org/obo/gaz.owl http://build.berkeleybop.org/job/build-gaz/lastSuccessfulBuild/artifact/gaz.obo |
http://gensc.org/gc_wiki/index.php/GAZ_Project | SCR_000473 | 2026-02-14 01:59:46 | 1 | ||||||
|
Denver University Department of Psychology Resource Report Resource Website |
Denver University Department of Psychology (RRID:SCR_000474) | data or information resource, organization portal, portal, department portal | The department of psychology at Denver University that offers degrees at the undergraduate, graduate and doctoral level. The doctoral programs have specializations such as Affect/Social, Child Clinical, Cognitive, and Developmental. | psychology, graduate, doctoral, affect, social, child, clinical, cognitive, developmental, neuroscience | has parent organization: University of Denver; Colorado; USA | nif-0000-01928 | SCR_000474 | DU Dept. of Psychology, University of Denver Department of Psychology | 2026-02-14 01:59:44 | 0 | |||||||||
|
ECNP Resource Report Resource Website 1+ mentions |
ECNP (RRID:SCR_000501) | ECNP | data or information resource, portal, community building portal | A pan-European scientific association to encourage research across the neurosciences and to translate new knowledge on fundamental disease mechanisms into new medicines and clinical applications. As an interdisciplinary forum for the science and treatment of disorders of the brain, they promote the communication and cross- fertilization of high-quality experimental and clinical research across the field of neuroscience. ECNP is a non-profit member-based association, independently governed and self-funded. ECNP is a public-interest-serving entity. | brain, neuroscience, disease mechanism, medicine, clinical, disease | is parent organization of: Preclinical Data Forum Network | Brain disorder | nlx_158605 | SCR_000501 | European College of Neuropsychopharmacology, ECNP - neuroscience applied | 2026-02-14 01:59:45 | 1 | |||||||
|
SpeedSeq Resource Report Resource Website 1+ mentions |
SpeedSeq (RRID:SCR_000469) | software resource | Software for a lightweight, flexible, and open source pipeline that identifies genomic variation (single nucleotide variants (SNVs), indels, and structural variants (SVs)). | standalone software |
is listed by: OMICtools has parent organization: University of Virginia; Virginia; USA |
Free, Available for download, Freely available | OMICS_04673 | SCR_000469 | 2026-02-14 01:59:44 | 7 | |||||||||
|
Health Level Seven International Resource Report Resource Website |
Health Level Seven International (RRID:SCR_000466) | HL7 | institution | ANSI-accredited standards developing organization providing a comprehensive framework and related standards for the exchange, integration, sharing, and retrieval of electronic health information that supports clinical practice and the management, delivery and evaluation of health services. HL7's 2,300+ members include approximately 500 corporate members who represent more than 90% of the information systems vendors serving healthcare. HL7 provides standards for interoperability that improve care delivery, optimize workflow, reduce ambiguity and enhance knowledge transfer among all of their stakeholders, including healthcare providers, government agencies, the vendor community, fellow SDOs and patients. | health care, interoperability, health, health service, clinical, management | is parent organization of: Health Level Seven Reference Implementation Model Version 3 | nlx_157307, Wikidata: Q17054989, grid.434932.b | https://ror.org/029ga8k16 | SCR_000466 | 2026-02-14 01:59:43 | 0 | ||||||||
|
MPscan Resource Report Resource Website |
MPscan (RRID:SCR_000587) | MPscan | data access protocol, software resource, web service | Web tool for index free mapping of multiple short reads on a genome. | linux, macos, next-generation sequencing, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: ATGC: Montpellier bioinformatics platform |
Free, Available for download, Freely available | biotools:mpscan, OMICS_00670 | https://bio.tools/mpscan | SCR_000587 | MPscan: index free mapping of multiple short reads on a genome | 2026-02-14 01:59:49 | 0 | ||||||
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FluWikie.com Resource Report Resource Website |
FluWikie.com (RRID:SCR_000506) | data or information resource, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. Flu Wikie is a topical portal on the flu. Major categories include health, Flu Symptoms, Avian Influenza, Swine Flu, Cold, Vaccination, Pandemic, Vitamin D, and Immune System. Many articles on topic are included. | virus | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_22823 | SCR_000506 | Flu Wikie, FluWikie | 2026-02-14 01:59:45 | 0 | |||||||||
|
MATCHCLIP Resource Report Resource Website |
MATCHCLIP (RRID:SCR_000541) | MATCHCLIP | software resource | Software program that detects the precise break points of Copy number variations (CNVs) through a fuzzy string matching algorithm using both CIGAR and POS information. In case the two break points of a CNV are in repeated regions and the break points are not unique, it reports the range where the break points can slide. | breakpoint, deletion, duplication, exon sequencing, structural variation, next generation sequencing |
is listed by: OMICtools has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
PMID:23967014 | Free, Available for download, Freely available, | OMICS_02289 | SCR_000541 | matchclips2, MATCHCLIPS | 2026-02-14 01:59:48 | 0 | ||||||
|
Exonhit Therapeutics Resource Report Resource Website |
Exonhit Therapeutics (RRID:SCR_000493) | commercial organization | A drug and diagnostic discovery company. | drug, diagnostic, in vitro | is related to: PharmaCog | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_158329 | SCR_000493 | Diaxonhit, Exonhit Therapeutics SA, ExonHit Therapeutics S.A. | 2026-02-14 01:59:44 | 0 | ||||||||
|
TDARACNE Resource Report Resource Website |
TDARACNE (RRID:SCR_000498) | TDARACNE | software resource | Software package to infer gene regulatory networks from time-series measurements. The algorithm is expected to be useful in reconstruction of small biological directed networks from time course data. | microarray, time course |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02013 | SCR_000498 | TDARACNE - Network reverse engineering from time course data | 2026-02-14 01:59:45 | 0 | |||||||
|
Aging Portal Resource Report Resource Website |
Aging Portal (RRID:SCR_000496) | Aging | portal, catalog, data or information resource, database, topical portal | Portal devoted to aging relevant scientific data and resources. | late adult human, senescence |
uses: Aging Genes and Interventions Database uses: anage uses: Human Life-Table Database uses: Gene Ontology uses: Grants.gov uses: Integrated Blogs uses: Integrated Clinical Trials uses: Integrated Videos uses: Integrated Grants uses: Lifespan Observations Database uses: One Mind Biospecimen Bank Listing uses: Gait in Parkinson's Disease uses: SciCrunch Registry has parent organization: SciCrunch |
Aging | NIA 1R03AG043018-01 | Restricted | nlx_158366 | SCR_000496 | 2026-02-14 01:59:47 | 0 | ||||||
|
Bio-derived Feedstocks for Sustainable UK-Based Manufacture of Chemicals and Pharmaceutical Intermediates Resource Report Resource Website |
Bio-derived Feedstocks for Sustainable UK-Based Manufacture of Chemicals and Pharmaceutical Intermediates (RRID:SCR_000490) | BFSUKMCPI | data or information resource, organization portal, portal, consortium | Project aiming to establish a range of new technologies to enable the synthesis of a range of chemicals from sugar beet pulp (SBP) in a cost-effective and sustainable manner. The chemical and pharmaceutical industries are currently reliant on petrochemical derived intermediates for the synthesis of a wide range of valuable products. Decreasing petrochemical reserves and concerns over costs and greenhouse gas emissions are driving the search for renewable sources of organic synthons. The UK is self-sufficient in the production of SBP which is a by-product of sugar beet production (8 million tonnes grown per year) and processing. The ability to convert SBP into chemicals and pharmaceutical intermediates will therefore have significant economic and environmental benefits. SBP is rich in carbohydrate (nearly 80% by weight) which is made up of roughly equal proportions of 2 biological polymers; cellulose and pectin. To be cost-effective it will be necessary to find uses for each of these substances. The consortium will develop a biorefinery approach for the selective breakdown of both polymers, purification of the breakdown compounds and their use to synthesize a range of added value products such as speciality chemicals, pharmaceuticals and biodegradable polymers. It is already known that cellulose can be broken down into hexose sugars and fermented to ethanol for use in biofuels. The focus is on the release of galacturonic acid and arabinose (from pectin) and their conversion, by chemical or enzymatic means, into added value products. Synthetic Biology methods will also be explored to test the feasibility of metabolically engineering microbial cells to simultaneously breakdown the polymeric feed material and synthesize a desired product, such as aromatic compounds, in a single integrated process. In conducting this research the consortium will adopt a holistic, systems-led, approach to biorefinery design and operation. Computer-based modelling tools will be used to assess the efficiency of raw material, water and energy utilization. Economic and Life Cycle Analysis (LCA) approaches will then be employed to identify the most cost-effective and environmentally benign product and process combinations. The project is supported by a range of industrial partners from raw material producer to intermediate technology providers and end-user chemical and pharmaceutical companies. This is crucial in providing business and socio-economic insights regarding the adoption of renewable resources into their current product portfolios. The company partners will also provide the material and equipment resources for the large-scale verification of project outcomes and their ultimate transition into commercial manufacture. The Intellectual Property (IP) expected to be generated by the consortium will most likely be related to new biocatalysts, synthetic routes, USD devices and modelling software. The data is accessible programmatically using one of three application programming interfaces GtR, GtR-2 and CERIF. | chemical, drug, drug development, pharmaceutical, manufacture, product development, sugar beet pulp, sugar beet, polymer, galacturonic acid, arabinose, biorefinery, cellulose, pectin, ethanol, biofuel |
is listed by: Consortia-pedia has parent organization: University College London; London; United Kingdom |
EPSRC | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_158450 | SCR_000490 | 2026-02-14 01:59:45 | 0 | |||||||
|
Mfuzz Resource Report Resource Website 10+ mentions |
Mfuzz (RRID:SCR_000523) | software resource | Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | r, time series, gene expression, clustering, microarray, preprocessing, time course, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Humboldt University of Berlin; Berlin; Germany has parent organization: Bioconductor |
PMID:18084642 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mfuzz, OMICS_02012 | https://bio.tools/mfuzz | http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz/ | SCR_000523 | Mfuzz - Soft clustering of time series gene expression data | 2026-02-14 01:59:45 | 14 | |||||
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Pindel Resource Report Resource Website 10+ mentions |
Pindel (RRID:SCR_000560) | Pindel | software resource | Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | deletion, insertion, nucleotide, genome, read, inversion, tandem duplication, structural variant, next-generation sequencing, pattern growth, indel, breakpoint, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA works with: cgpPindel |
PMID:19561018 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:pindel, OMICS_00321 | https://bio.tools/pindel | SCR_000560 | 2026-02-14 01:59:46 | 22 | ||||||
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OntoMorph Tab Resource Report Resource Website |
OntoMorph Tab (RRID:SCR_000443) | data analysis software, software resource, data processing software, software application | OntoMorph is a tab plugin for Protege-OWL 3 that allows a user to mark-up portions of a Neurolucida neuron morphology with OWL instances. A user loads a Neurolucida morphology file, either from their hard drive or from an arbitrary URL, into an interface that allows them to zoom, rotate, and translate the morphology. The interface allows them to select points on the morphology to indicate points, segments, or subtrees of the morphology they wish to assign to an OWL instance. After this selection has been made, OntoMorph saves the selection to the currently active OWL instance in the ontology that is currently loaded into Protege. No modifications are made to the Neurolucida file itself. As a result, an association is created between that portion of the morphology and the OWL instance, such that selecting the OWL instance allows retrieval of the portion. Upon retrieval, the morphology portion can be highlighted, so the user can keep track of what pieces each instance refer to. | annotation, java, morphology, neurolucida, neuron, neuroscience, plugin, protege, software, ontology, owl | has parent organization: University of California at San Diego; California; USA | Free, Available for download, Freely available | nif-0000-24916 | SCR_000443 | OntoMorph | 2026-02-14 01:59:43 | 0 | ||||||||
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SiPhy Resource Report Resource Website 1+ mentions |
SiPhy (RRID:SCR_000564) | SiPhy | sequence analysis resource | Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions. | java, mutation, phylogeny, substitution pattern, mutation rate |
is listed by: OMICtools has parent organization: Broad Institute |
NHGRI ; NSF |
PMID:19478016 | Free, Available for download, Freely available, | OMICS_00183 | SCR_000564 | 2026-02-14 01:59:46 | 6 | ||||||
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TNO-DECO Resource Report Resource Website |
TNO-DECO (RRID:SCR_000440) | software resource | Matlab code for preprocessing gas chromatography mass spectrometry data. | matlab, mass spectrometry | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_02660 | SCR_000440 | 2026-02-14 01:59:44 | 0 | |||||||||
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Scaffold builder Resource Report Resource Website |
Scaffold builder (RRID:SCR_000556) | scaffold_builder | data analysis service, production service resource, service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Tool designed to generate scaffolds (super contigs of sequences joined by N-bases) using the homology provided by a closely related reference sequence. Scaffold_builder is an advanced wrapper for Nucmer, written in Python that resolves several situations that may arise when mapping contigs to the reference genome. | scaffolding |
is listed by: OMICtools has parent organization: San Diego Supercomputer Center |
PMID:24267787 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00046 | SCR_000556 | 2026-02-14 01:59:46 | 0 | |||||||
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SNPiR Resource Report Resource Website 1+ mentions |
SNPiR (RRID:SCR_000557) | SNPiR | software resource | Software for reliable Identification of Genomic Variants Using RNA-seq Data. | genomic variant, rna-seq |
is listed by: OMICtools has parent organization: Stanford University; Stanford; California |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01362 | SCR_000557 | SNPiR: Reliable Identification of Genomic Variants Using RNA-seq Data | 2026-02-14 01:59:48 | 1 |
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