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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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AraCyc Resource Report Resource Website 50+ mentions |
AraCyc (RRID:SCR_008109) | data repository, service resource, storage service resource, database, data or information resource | Curated species-specific database present at the Plant Metabolic Network. It has a large number of experimentally supported enzymes and metabolic pathways, but it also houses a substantial number of computationally predicted enzymes and pathways. | enzyme, gene, arabidopsis thaliana, biochemical, pathway, reaction, metabolism, metabolic pathway, data set, data analysis service, web service, FASEB list |
is used by: Arabidopsis Reactome is listed by: 3DVC has parent organization: Plant Metabolic Network |
NSF | PMID:12805578 PMID:15888675 |
The community can contribute to this resource | nif-0000-20811 | http://www.arabidopsis.org/biocyc/index.jsp http://www.plantcyc.org |
SCR_008109 | Arabidopsis enzymes and biochemical pathways database | 2026-02-12 09:44:46 | 69 | |||||
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OpenWetWare Resource Report Resource Website 1+ mentions |
OpenWetWare (RRID:SCR_008053) | OWW | wiki, blog, experimental protocol, narrative resource, community building portal, data or information resource, portal | OpenWetWare is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering. OWW provides a place for labs, individuals, and groups to organize their own information and collaborate with others easily and efficiently. In the process, the hope is that OWW will not only lead to greater collaboration between member groups, but also provide a useful information portal to our colleagues, and ultimately the rest of the world. OWW''s approaches to achieve their goals: # Lower the technical barriers to sharing and dissemination of knowledge in biological research # Build a community of researchers in biology and biological engineering that values, practices, and innovates the open sharing of information # Integrate OpenWetWare into existing and future reward structures in research | biological engineering, biological research, biology, collaboration, community, information, lab, portal, sharing, structure, material resource, media, enzyme, buffer, reporter, page, fixative, detergent, electrophoresis, agarose gel electrophoresis, protease, acid, base, rna polymerases, antibiotic, chemical, rna polymerase, dna ligase, dna polymerase, phosphatase, dye, stain, fluorescent protein | has parent organization: BioBricks Foundation | NSF ; Massachusetts Institute of Technology; Massachusetts; USA |
nif-0000-10393 | SCR_008053 | 2026-02-12 09:44:37 | 3 | ||||||||
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Viking Viewer for Connectomics Resource Report Resource Website 10+ mentions |
Viking Viewer for Connectomics (RRID:SCR_005986) | software resource, data management software, software application, data processing software, collaboration tool | A web-compliant application that allows connectomics visualization by converting datasets to web-optimized tiles, delivering volume transforms to client devices, and providing groups of users with connectome annotation tools and data simultaneously via conventional internet connections. Viking is an extensible tool for connectomics analysis and is generalizable to histomics applications. | annotation, 2d image, microscopy image, volume, serial section, 3d reconstruction, segmentation, microscopy, visualization, optical imaging, connectomics, synapse, retina, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: 3DVC has parent organization: University of Utah; Utah; USA |
Research to Prevent Blindness ; University of Utah; Utah; USA ; Graduate Research Fellowship ; Utah Science Technology and Research Initiative ; NEI R01 EY02576; NEI R01 EY015128; NEI P01 EY014800; NSF 0941717; NIDCD T32DC008553; NIBIB EB005832 |
PMID:21118201 | Open source | nlx_151360 | http://www.nitrc.org/projects/viking_viewer | SCR_005986 | Viking, Viking Connectome Annotation System, Viking Annotation System | 2026-02-12 09:44:22 | 14 | |||||
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crowdLabs Resource Report Resource Website 1+ mentions |
crowdLabs (RRID:SCR_006294) | crowdLabs | analysis service resource, service resource, production service resource, storage service resource, community building portal, data analysis service, data or information resource, portal | A social visualization repository for the scientific workflow management system VisTrails providing a platform for sharing and executing computational tasks. It adopts the model used by social Web sites and that integrates a set of usable tools and a scalable infrastructure to provide an environment for scientists to collaboratively analyze and visualize data. crowdLabs aims to foster collaboration but was specifically designed to support the needs of computational scientists, including the ability to access high-performance computers and manipulate large volumes of data. By providing mechanisms that simplify the publishing and use of analysis pipelines, it allows IT personnel and end users to collaboratively construct and refine portals. This lowers the barriers for the use of scientific analyses and enables broader audiences to contribute insights to the scientific exploration process, without the high costs incurred by traditional portals. In addition, it supports a more dynamic environment where new exploratory analyses can be added on-the-fly. | platform, computation, data sharing |
is listed by: FORCE11 is related to: VisTrails |
NSF | nif-0000-06716 | http://www.force11.org/node/4666 | SCR_006294 | crowd Labs | 2026-02-12 09:44:21 | 1 | ||||||
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PHYLIP Resource Report Resource Website 1000+ mentions |
PHYLIP (RRID:SCR_006244) | PHYLIP | source code, software application, software resource, data processing software | A free package of software programs for inferring phylogenies (evolutionary trees). The source code is distributed (in C), and executables are also distributed. In particular, already-compiled executables are available for Windows (95/98/NT/2000/me/xp/Vista), Mac OS X, and Linux systems. Older executables are also available for Mac OS 8 or 9 systems. | phylogeny prediction, evolutionary tree, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Washington; Seattle; USA works with: PAML |
NSF ; NIGMS ; DOE |
Free | nif-0000-06708, OMICS_04240, biotools:phylip | https://bio.tools/phylip https://sources.debian.org/src/phylip/ |
SCR_006244 | PHYLogeny Inference Package | 2026-02-12 09:44:20 | 3519 | |||||
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Guppy Project Resource Report Resource Website 1+ mentions |
Guppy Project (RRID:SCR_006255) | Guppy Project | topical portal, video resource, organism-related portal, data or information resource, portal | A project that observes the processes of adaptive evolution in nature, and tests evolutionary hypotheses, by studying populations of guppies on the Caribbean island of Trinidad. Darwin thought that evolution by natural selection occurred very slowly, over hundreds if not thousands of years. Evolutionary biologists now know that evolutionary changes in species can happen very quickly, over a relatively few generations. The National Science Foundation (NSF), through its Integrative Biological Research (FIBR) program, is funding a 5-year study by 13 biologists from colleges, universities, and research institutions throughout the United States and Canada, to study the relationship of adaptive evolution and environmental circumstances. The Trinidadian guppy (Poecilia reticulata) is an excellent species for these purposes because: * It matures rapidly (one generation = 3-4 months) * It inhabits different ecological environments that can be easily manipulated On Trinidad, guppies live in streams, or portions of streams, that can differ in the species of predators that the guppies have to contend with. Some streams are high-predation environments, others low-predation. Different predation environments are often right next to one another, separated by a waterfall (which neither guppies nor predators can cross). Guppies from high-predation environments experience much higher mortality rates than do guppies in low-predation environments. High mortality is associated with the following characteristics, all of which have a genetic basis: * Earlier maturity * Greater investment of resources in reproduction * More and smaller offspring. We have found that mortality rates can be manipulated by: * Transplanting guppies from high-predation localities into sites from which they and their predators had previously been excluded by natural waterfalls, thus lowering mortality rates; * Introducing predators into low-predation sites, thus increasing mortality rates. Such experiments have shown that species evolve as predicted by theory. We have also found that evolution by natural selection can be remarkably fast, on the order of four to seven orders of magnitude faster than had been inferred from the fossil record. | adaption, evolution, adaptive evolution, environment, trinidadian guppy, poecilia reticulata, image, natural selection | has parent organization: University of California at Riverside; California; USA | NSF | nlx_151840 | SCR_006255 | 2026-02-12 09:44:12 | 6 | ||||||||
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Plant Ontology Resource Report Resource Website 10+ mentions |
Plant Ontology (RRID:SCR_006494) | PO | data or information resource, database, ontology, controlled vocabulary | Ontology and database that links plant anatomy, morphology and growth and development to plant genomics data.Plant Ontology Consortium develops, curates and shares controlled vocabularies (ontologies) that describe plant structures and growth and developmental stages, providing semantic framework for meaningful cross species queries across databases. PO is under active development to expand to encompass terms and annotations from all plants. | obo, gene, development, anatomy, morphology, growth, genomics, database |
has parent organization: Oregon State University; Oregon; USA has parent organization: Cornell University; New York; USA |
NSF 0822201; NSF 0321685 |
PMID:18628842 PMID:18194960 |
SCR_006844, nlx_55564 | SCR_006494 | Plant Ontology Browser, PO Browser, Plant Ontology Consortium Database, PO Database, Plant Ontology Database, POC Database | 2026-02-12 09:44:25 | 31 | ||||||
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Integrated Earth Data Applications Resource Report Resource Website 1+ mentions |
Integrated Earth Data Applications (RRID:SCR_006739) | IEDA | analysis service resource, data repository, service resource, production service resource, storage service resource, database, data analysis service, data or information resource | A community-based data facility to support, sustain, and advance the geosciences by providing data services for observational solid earth data from the Ocean, Earth, and Polar Sciences. IEDA systems enable these data to be discovered and reused by a diverse community now and in the future. Data services include data access, data analysis, data compliance, data publication, DOI search, and web services. Desktop apps GeoMapApp and Virtual Ocean are available to explore, visualize and analyze your own data within the context of hundreds of other earth science data from around the world. IEDA is a partnership between EarthChem and the Marine Geoscience Data System (MGDS). EarthChem and MGDS systems include the geochemical databases PetDB and SedDB, the geochemistry data network EarthChem, the Ridge2000 and MARGINS Data Portals, the Academic Seismic Portal field data collection, the Antarctic and Southern Ocean Data System, the Global Multi Resolution Topography synthesis, and the System for Earth Sample Registration SESAR. | map, ocean, earth, polar, sciences, ocean sciences, earth sciences, polar sciences, doi, global geochemistry, marine geoscience |
has parent organization: Columbia University; New York; USA is parent organization of: Marine Geoscience Data System is parent organization of: Global-Multi Resolution Topography Image Service is parent organization of: Global-Multi Resolution Topography Grid Service |
NSF | The community can contribute to this resource, Free, Open unspecified license | nlx_156096 | SCR_006739 | 2026-02-12 09:44:34 | 1 | |||||||
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Ribosomal Database Project Resource Report Resource Website 1000+ mentions |
Ribosomal Database Project (RRID:SCR_006633) | RDP | data or information resource, database, resource | A database which provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences. It specifically contains information on quality-controlled, aligned and annotated bacterial and archaean 16S rRNA sequences, fungal 28S rRNA sequences, and a suite of analysis tools for the scientific community. Most of the RDP tools are now available as open source packages for users to incorporate in their local workflow. | microbiome, database, rrna gene sequence, rrna, ribosome, genome browser, high-throughput sequencing, bacteria, archaea, fungi, FASEB list |
is listed by: OMICtools is listed by: Human Microbiome Project has parent organization: Michigan State University; Michigan; USA is parent organization of: RDPipeline |
DOE DE-FG02-99ER62848; DOE DE-SC0004601; DOE DE-FC02-07ER64494; NIEHS P42 ES004911; NSF DBI-0328255; USDA 2008-35107-04542; NHLBI U01HL098961; NIDDK UH3 DK083993 |
PMID:24288368 PMID:17586664 |
Open source | r3d100012372, nif-0000-03404, OMICS_01513 | https://doi.org/10.17616/R3C087 | SCR_006633 | Ribosomal Database Project | 2026-02-12 09:44:33 | 1441 | ||||
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Ligand Expo Resource Report Resource Website |
Ligand Expo (RRID:SCR_006636) | data or information resource, database, resource | An integrated data resource for finding chemical and structural information about small molecules bound to proteins and nucleic acids within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry. A sketch tool is also provided for building new chemical definitions from reported PDB chemical components. | element, fingerprint, formula, amino acid, aromatic ring, atom, bound, carbon, chemical, component, depot, ligand, molecular, molecule, nitrogen, nucleic acid, nucleotide, pharmaceutical, protein, small molecule, structure, macromolecule, model |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: Worldwide Protein Data Bank (wwPDB) has parent organization: Rutgers University; New Jersey; USA has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
NSF ; NIGMS ; DOE ; NLM ; NCI ; NCRR ; NIBIB ; NINDS ; NIDDK |
PMID:15059838 | nif-0000-21237, OMICS_02751 | http://ligand-depot.rutgers.edu/ | SCR_006636 | Ligand Depot | 2026-02-12 09:44:17 | 0 | ||||||
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Rice Genome Annotation Resource Report Resource Website 1000+ mentions |
Rice Genome Annotation (RRID:SCR_006663) | Osa1 | analysis service resource, service resource, production service resource, database, data analysis service, data or information resource | Database and resource that provides sequence and annotation data for the rice genome. This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 75 tracks of annotation. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads. Rice is a model species for the monocotyledonous plants and the cereals which are the greatest source of food for the world''s population. While rice genome sequence is available through multiple sequencing projects, high quality, uniform annotation is required in order for genome sequence data to be fully utilized by researchers. The existence of a common gene set and uniform annotation allows researchers within the rice community to work from a common resource so that their results can be more easily interpreted by other scientists. The objective of this project has always been to provide high quality annotation for the rice genome. They generated, refined and updated gene models for the estimated 40,000-60,000 total rice genes, provided standardized annotation for each model, linked each model to functional annotation including expression data, gene ontologies, and tagged lines. They have provided a resource to extend the annotation of the rice genome to other plant species by providing comparative alignments to other plant species. Analysis/Tools are available including: BLAST, Locus Name Search, Functional Term Search, Protein Domain Search, Anatomy Expression Viewer, Highly Expressed Genes | rice, oryza sativa, maize, corn, zea mays, wheat, triticum aestivum, gene, genome, annotation, FASEB list |
is listed by: OMICtools has parent organization: Michigan State University; Michigan; USA |
NSF DBI-0321538; NSF DBI-0834043 |
PMID:17145706 | Acknowledgement requested | OMICS_01563, nif-0000-31459 | http://rice.tigr.org | http://rice.plantbiology.msu.edu/pseudomolecules/info.shtml | SCR_006663 | Rice Genome Annotation Project, MSU Rice Genome Annotation Project Database and Resource | 2026-02-12 09:44:34 | 1423 | |||
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REDfly Regulatory Element Database for Drosophilia Resource Report Resource Website 10+ mentions |
REDfly Regulatory Element Database for Drosophilia (RRID:SCR_006790) | REDfly | data repository, service resource, storage service resource, database, data or information resource | Curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). Includes experimentally verified fly regulatory elements along with their DNA sequence, associated genes, and expression patterns they direct. Submission of experimentally verified cis-regulatory elements that are not included in REDfly database are welcome. | transcriptional cis-regulatory module, transcription factor binding site, dna sequence, gene, expression pattern, genome, gene expression, transcription factor, cis-regulatory module, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Drosophila anatomy and development ontologies is related to: FlyMine has parent organization: University at Buffalo; New York; USA |
NSF EF0843229; NIGMS U24 GM144232 |
PMID:20965965 PMID:18039705 PMID:16303794 |
Acknowledgement requested | OMICS_01870, biotools:redfly, nif-0000-03393 | https://bio.tools/redfly | SCR_006790 | Regulatory Element Database for Drosophilia, Regulatory Element Database | 2026-02-12 09:44:24 | 14 | ||||
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Karma Resource Report Resource Website 50+ mentions |
Karma (RRID:SCR_003732) | Karma | software application, software resource, data management software | An information integration software tool that enables users to integrate data from a variety of data sources including databases, spreadsheets, delimited text files, XML, JSON, KML and Web APIs. Users integrate information by modeling it according to an ontology of their choice using a graphical user interface that automates much of the process. Karma learns to recognize the mapping of data to ontology classes and then uses the ontology to propose a model that ties together these classes. Users then interact with the system to adjust the automatically generated model. During this process, users can transform the data as needed to normalize data expressed in different formats and to restructure it. Once the model is complete, users can publish the integrated data as RDF or store it in a database. | integration, FASEB list |
is related to: GitHub has parent organization: University of Southern California; Los Angeles; USA |
Air Force Research Laboratory FA8750-14-C-0240; NCRR 1 U24 RR025736-01; NCRR 1 UL1 RR031986-01; NSF IIS-1117913; NSF CMMI-0753124 |
PMID:15215426 | Apache License, v2 | nlx_157923 | https://github.com/InformationIntegrationGroup/Web-Karma | SCR_003732 | Karma A Data Integration Tool, Karma - A Data Integration Tool | 2026-02-12 09:43:39 | 83 | ||||
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Yogo Data Management System Resource Report Resource Website |
Yogo Data Management System (RRID:SCR_004239) | source code, software application, software resource, software toolkit | A set of software tools created to rapidly build scientific data-management applications. These applications will enhance the process of data annotation, analysis, and web publication. The system provides a set of easy-to-use software tools for data sharing by the scientific community. It enables researchers to build their own custom-designed data management systems. The problem of scientific data management rests on several challenges. These include flexible data storage, a way to share the stored data, tools to curate the data, and history of the data to show provenance. The Yogo Framework gives you the ability to build scientific data management applications that address all of these challenges. The Yogo software is being developed as part of the NeuroSys project. All tools created as part of the Yogo Data Management Framework are open source and released under an OSI approved license. | has parent organization: Montana State University | The Michael J. Fox Foundation for Parkinsons Research ; Lumina Foundation ; NSF ; EPSCoR Program ; Montana State University; Montana; USA ; NIMH MH0441-07 |
Open unspecified license | nlx_25179 | SCR_004239 | Yogo Framework, Yogo Data Management Framework, Yogo | 2026-02-12 09:43:46 | 0 | ||||||||
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Open Connectome Project Resource Report Resource Website 1+ mentions |
Open Connectome Project (RRID:SCR_004232) | Open Connectome Project | analysis service resource, source code, data access protocol, data repository, software resource, service resource, web service, production service resource, image repository, storage service resource, data analysis service, data or information resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Connectomes repository to facilitate the analysis of connectome data by providing a unified front for connectomics research. With a focus on Electron Microscopy (EM) data and various forms of Magnetic Resonance (MR) data, the project aims to make state-of-the-art neuroscience open to anybody with computer access, regardless of knowledge, training, background, etc. Open science means open to view, play, analyze, contribute, anything. Access to high resolution neuroanatomical images that can be used to explore connectomes and programmatic access to this data for human and machine annotation are provided, with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access, so collectively, we can begin to unravel connectomes. Services: * Data Hosting - Their Bruster (brain-cluster) is large enough to store nearly any modern connectome data set. Contact them to make your data available to others for any purpose, including gaining access to state-of-the-art analysis and machine vision pipelines. * Web Viewing - Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by Google Maps, enhanced to allow the exploration of 3D image data. View the fork of the code or go directly to view the data. * Volume Cutout Service - RESTful API that enables you to select any arbitrary volume of the 3d database (3ddb), and receive a link to download an HDF5 file (for matlab, C, C++, or C#) or a NumPy pickle (for python). Use some other programming language? Just let them know. * Annotation Database - Spatially co-registered volumetric annotations are compactly stored for efficient queries such as: find all synapses, or which neurons synapse onto this one. Create your own annotations or browse others. *Sample Downloads - In addition to being able to select arbitrary downloads from the datasets, they have also collected a few choice volumes of interest. * Volume Viewer - A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels. The code and program can be downloaded. * Machine Vision Pipeline - They are building a machine vision pipeline that pulls volumes from the 3ddb and outputs neural circuits. - a work in progress. As soon as we have a stable version, it will be released. * Mr. Cap - The Magnetic Resonance Connectome Automated Pipeline (Mr. Cap) is built on JIST/MIPAV for high-throughput estimation of connectomes from diffusion and structural imaging data. * Graph Invariant Computation - Upload your graphs or streamlines, and download some invariants. * iPad App - WholeSlide is an iPad app that accesses utilizes our open data and API to serve images on the go. | human, primary visual cortex, data sharing, male, electron microscopy, mri, connectome, annotation, image collection, array tomography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CATMAID is related to: neurodata is parent organization of: Rambo3D |
Johns Hopkins University; Maryland; USA ; JHU Applied Research Laboratory IRAD ; JHU Whiting School of Engineering ; Dean's Award ; NIBIB 1RO1EB016411-01 (CRCNS); DARPA N66001-14-1-4028 (GRAPHS); NSF ACI-1261715; NSF OCI-1040114; NIDA 1R01DA036400-01; |
PMID:23707591 | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000189, nlx_143645 | http://openconnecto.me http://www.nitrc.org/projects/ocp/ |
SCR_004232 | openconnectomeproject, Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time., Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time | 2026-02-12 09:43:46 | 7 | ||||
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DigiMorph Resource Report Resource Website 50+ mentions |
DigiMorph (RRID:SCR_004416) | DigiMorph | training material, database, narrative resource, video resource, data or information resource, image | A dynamic archive of information on digital morphology and high-resolution X-ray computed tomography of biological specimens serving imagery for more than 750 specimens contributed by almost 150 collaborating researchers from the world''s premiere natural history museums and universities. Browse through the site and see spectacular imagery and animations and details on the morphology of many representatives of the Earth''s biota. Digital Morphology, part of the National Science Foundation Digital Libraries Initiative, develops and serves unique 2D and 3D visualizations of the internal and external structure of living and extinct vertebrates, and a growing number of ''invertebrates.'' The Digital Morphology library contains nearly a terabyte of imagery of natural history specimens that are important to education and central to ongoing cutting-edge research efforts. Digital Morphology visualizations are now in use in classrooms and research labs around the world and can be seen in a growing number of museum exhibition halls. The Digital Morphology site currently presents: * QuickTime animations of complete stacks of serial CT sections * Animated 3D volumetric movies of complete specimens * Stereolithography (STL) files of 3D objects that can be viewed interactively and rapidly prototyped into scalable physical 3D objects that can be handled and studied as if they were the original specimens * Informative introductions to the scanned organisms, often written by world authorities * Pertinent bibliographic information on each specimen * Useful links * A course resource for our ''Digital Methods for Paleontology'' course, in which students learn how to generate all of the types of imagery displayed on the Digital Morphology site | image archive, x-ray computed tomographic scanner, x-ray computed tomography, scientific name, common name, cladogram, dinosaur, tapir, horned lizard, endocast, bat, primate, FASEB list | has parent organization: University of Texas at Austin; Texas; USA | NSF | The images may be used for the personal education of website visitors. Any commercial reproduction, Redistribution, Publication, Or other use of the website content, By electronic means or otherwise, Is prohibited unless pursuant to a written agreement signed by the copyright holder. | nlx_143746, r3d100011511 | https://doi.org/10.17616/R3TD0C | SCR_004416 | Digital Morphology library, Digital Morphology | 2026-02-12 09:43:51 | 74 | |||||
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Catalog of Fishes Resource Report Resource Website |
Catalog of Fishes (RRID:SCR_004408) | CASGEN, CASSPC, CASREF, | book, bibliography, database, narrative resource, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. The Catalog of Fishes is the authoritative reference for taxonomic fish names, featuring a searchable on-line database. The Catalog of Fishes covers more than 53,000 species and subspecies, over 10,000 genera and subgenera, and includes in excess of 16,000 bibliographic references. The Catalog of Fishes consists of three hardbound volumes of 900-1000 pages each, along with a CD-ROM. The online database is updated about every 8 weeks and is now about twice the size of the published version. It is one of the oldest and most complete databases for any large animal group. References are over 30,000. Valid species are over 30,000. This work is an essential reference for taxonomists, scientific historians, and for any specialist dealing with fishes. Entries for species, for example, consist of species/subspecies name, genus, author, date, publication, pages, figures, type locality, location of type specimen(s), current status (with references), family/subfamily, and important publication, taxonomic, or nomenclatural notes. Nearly all original descriptions have been examined, and much effort has gone into determining the location of type specimens. The Genera are updated from Eschmeyer''s 1990 Genera of Recent Fishes. Both genera and species are listed in a classification using recent taxonomic schemes. Also included are a lengthy list of museum acronyms, an interpretation of the International Code of Zoological Nomenclature, and Opinions of the International Commission involving fishes. | genus, species, reference, publication |
is related to: Teleost Taxonomy Ontology is related to: Phenoscape Knowledgebase has parent organization: California Academy of Sciences |
NSF ; Alfred P. Sloan Foundation |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_41737 | SCR_004408 | Catalog of Fishes database | 2026-02-12 09:43:50 | 0 | ||||||
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PGN Resource Report Resource Website |
PGN (RRID:SCR_004559) | PGN | analysis service resource, data repository, service resource, production service resource, storage service resource, database, data analysis service, data or information resource, data set | Resource for the storage, retrieval and annotation of plant ESTs, with a focus on comparative genomics. PGN comprises an analysis pipeline and a website, and presently contains mainly data from the Floral Genome Project. However, it accepts submission from other sources. All data in PGN is directly derived from chromatograms and all original and intermediate data are stored in the database. The current datasets on PGN come from the floral genome project and includes the following species: Acorus americanus, Amborella trichopoda, Asparagus officinalis, Cucumis sativus, Eschscholzia californica, Eschscholzia californica, Illicium parviflorum, Ipomopsis aggregata, Liriodendron tulipifera, Mesembryanthemum crystallinum, Mimulus guttatus, Nuphar advena, Papaver somniferum, Persea americana, Prymnesium parvum, Ribes americanum, Saruma henryi, Stenogyne rugosa, Vaccinium corymbosa, Welwitschia mirabilis, Yucca filamentosa, Zamia fischeri. For functional annotation, blast is used to compare find the best match of each unigene sequence to in the Genbank NR database, and the in complete coding sequences from Arabidopsis. These annotations are stored in the database and serve as the primary source of annotation. The annotation framework will be extended to Gene Ontology annotations in the future. | expressed sequence tag, genomics, functional annotation, blast, sequencing, chromatogram | has parent organization: Cornell University; New York; USA | NSF DBI-9872617; NSF DBI-0115684 |
nlx_55223 | SCR_004559 | PGN - Plant Genome Network, Plant Genome Network | 2026-02-12 09:43:53 | 0 | |||||||
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UBERON Resource Report Resource Website 50+ mentions |
UBERON (RRID:SCR_010668) | UBERON | data or information resource, ontology, controlled vocabulary | An integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. Uberon consists of over 10000 classes (March 2014) representing structures that are shared across a variety of metazoans. The majority of these classes are chordate specific, and there is large bias towards model organisms and human. | anatomy, comparative, evolution, organ system, anatomical structure, body part, organ, tissue, body, vertebrate, function, phenotype, expression, model organism, obo |
is used by: Neuroscience Information Framework is listed by: BioPortal is related to: Gene Ontology has parent organization: OBO |
ARRA ; NSF ; NHGRI 5R01HG004838; NHGRI P41HG002273; DOE DE-AC02-05CH11231; NCRR 1U24RR029825-01; NHGRI P41HG002273-09S1 |
PMID:22293552 | nlx_74404 | SCR_010668 | Uber anatomy ontology, Uber-anatomy ontology | 2026-02-12 09:45:13 | 59 | ||||||
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Brain Observatory Resource Report Resource Website |
Brain Observatory (RRID:SCR_010641) | Brain Observatory | service resource, topical portal, storage service resource, biospecimen repository, video resource, data or information resource, portal, material storage repository | Formerly a topical portal studying the brain which collected and imaged 1000 human brains, the Brain Observatory has partnered with the Institute for Brain and Society to build virtual laboratories that will feed directly into the database of images and knowledge created in the context of the Human Brain Library. The Brain Observatory will also host exhibits, conferences, and events aimed at promoting a heightened awareness of brain research and how its results can benefit personal brain fitness and mental health. | human, brain, visual cortex, neuroimaging | has parent organization: University of California San Diego School of Medicine; California; USA | Human immunodeficiency virus, NeuroAIDS, AIDS, Amnesia | NIMH ; NSF ; The Dana Foundation ; NEI |
Public | nlx_69083 | http://thebrainobservatory.ucsd.edu/ | SCR_010641 | The Brain Observatory | 2026-02-12 09:45:32 | 0 |
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