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http://www.biodas.org

The Distributed Annotation System (DAS) defines a communication protocol used to exchange annotations on genomic or protein sequences. It is motivated by the idea that such annotations should not be provided by single centralized databases, but should instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients. The advantages of this system are that control over the data is retained by data providers, data is freed from the constraints of specific organisations and the normal issues of release cycles, API updates and data duplication are avoided. DAS is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up sequence annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers. DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities. A DAS-enabled website or application can aggregate complex and high-volume data from external providers in an efficient manner. For the biologist, this means the ability to plug in the latest data, possibly including a user''s own data. For the application developer, this means protection from data format changes and the ability to add new data with minimal development cost. Here are some examples of DAS-enabled applications or websites for end users: :- Dalliance Experimental Web/Javascript based Genome Viewer :- IGV Integrative Genome Viewer java based browser for many genomes :- Ensembl uses DAS to pull in genomic, gene and protein annotations. It also provides data via DAS. :- Gbrowse is a generic genome browser, and is both a consumer and provider of DAS. :- IGB is a desktop application for viewing genomic data. :- SPICE is an application for projecting protein annotations onto 3D structures. :- Dasty2 is a web-based viewer for protein annotations :- Jalview is a multiple alignment editor. :- PeppeR is a graphical viewer for 3D electron microscopy data. :- DASMI is an integration portal for protein interaction data. :- DASher is a Java-based viewer for protein annotations. :- EpiC presents structure-function summaries for antibody design. :- STRAP is a STRucture-based sequence Alignment Program. Hundreds of DAS servers are currently running worldwide, including those provided by the European Bioinformatics Institute, Ensembl, the Sanger Institute, UCSC, WormBase, FlyBase, TIGR, and UniProt. For a listing of all available DAS sources please visit the DasRegistry. Sponsors: The initial ideas for DAS were developed in conversations with LaDeana Hillier of the Washington University Genome Sequencing Center.

Proper citation: Distributed Annotation System (RRID:SCR_008427) Copy   

•   Source: SciCrunch Registry

https://www.stat.auckland.ac.nz/~paul/plaudits/Iobion.htm

GeneTraffic is a web-based microarray data analysis and management software developed by Iobion Informatics that allows users to log onto a server, upload their microarray data and perform analysis and project management remotely. GeneTraffic was made by Iobion Informatics (now under Stratagene) and can be accessed thorough Internet Explorer 6.0 or greater on Windows XP.

Proper citation: GeneTraffic (RRID:SCR_008651) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/arrayexpress/

International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus.

Proper citation: ArrayExpress (RRID:SCR_002964) Copy   

•   Source: SciCrunch Registry

http://developingmouse.brain-map.org/

Map of gene expression in developing mouse brain revealing gene expression patterns from embryonic through postnatal stages. Provides information about spatial and temporal regulation of gene expression with database. Feature include seven sagittal reference atlases created with a developmental ontology. These anatomic atlases may be viewed alongside in situ hybridization (ISH) data as well as by itself.

Proper citation: Allen Developing Mouse Brain Atlas (RRID:SCR_002990) Copy   

•   Source: SciCrunch Registry

http://childes.talkbank.org/

Child language component of TalkBank system. TalkBank is system for sharing and studying conversational interactions. Includes software developed for speech recognition and analysis as well as behavior recognition. Database contains transcript and media data collected from conversations between young children and their playmates and caretakers. Conversations with older children and adults are available from TalkBank. All of data is transcribed in CHAT and CA/CHAT formats.

Proper citation: Child Language Data Exchange System (CHILDES) (RRID:SCR_003241) Copy   

•   Source: SciCrunch Registry

http://dash.harvard.edu/

Harvard University''s central service for sharing and preserving work. In addition to the scholarly journal articles targeted by Harvard''s several open access resolutions, DASH maybe used to self-archive manuscripts and materials. DASH supports a variety of file formats, and users are encouraged to deposit related materials with manuscripts (including data, images, audio and video files, etc.) When users deposit their work in DASH, it becomes visible to colleagues around the world by virtue of metadata harvesting, Google Scholar, and other indexing services. Higher visibility leads to higher rates of citation and impact. When users post early versions of their work, before publication, they establish intellectual priority sooner. Users act in their own best interests by taking part in the University''s mission to share and preserve the knowledge produced there. Because Harvard now has a prior, non-exclusive license to faculty journal articles in schools with open access policies, those faculty members are required to act accordingly when publishing journal articles, either by attaching an addendum to their publication agreement or obtaining a waiver. They then must deposit the publication in DASH.

Proper citation: Digital Access to Scholarship at Harvard (RRID:SCR_004122) Copy   

•   Source: SciCrunch Registry

http://mialab.mrn.org/index.html

MIALAB, headed by Dr. Vince Calhoun, focuses on developing and optimizing methods and software for quantitative analysis of structure and function in medical images with particular focus on the study of psychiatric illness. We work with many types of data, including functional magnetic resonance imaging (fMRI), diffusion tensor imaging (DTI), electroencephalography (EEG), structural imaging and genetic data. Much of our time is spent working on new methods for flexible analysis of brain imaging data. The use of data driven approaches is very useful for extracting potentially unpredictable patterns within these data. However such methods can be further improved by incorporating additional prior information as constraints, in order to benefit from what we know. To this end, we draw heavily from the areas of image processing, adaptive signal processing, estimation theory, neural networks, statistical signal processing, and pattern recognition.

Proper citation: MIALAB - Medical Image Analysis Lab (RRID:SCR_006089) Copy   

•   Source: SciCrunch Registry

http://www.chemspider.com/

Collection of chemical structures. Provides access to structures, properties and associated information from hundreds of data sources to find compounds of interest and provides services to improve this data by curation and annotation and to integrate it with users applications.

Proper citation: ChemSpider (RRID:SCR_006360) Copy   

•   Source: SciCrunch Registry

https://proteomecommons.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A public resource for sharing general proteomics information including data (Tranche repository), tools, and news. Joining or creating a group/project provides tools and standards for collaboration, project management, data annotation, permissions, permanent storage, and publication.

Proper citation: Proteome Commons (RRID:SCR_006234) Copy   

•   Source: SciCrunch Registry

http://edamontology.org/

An ontology of bioinformatics operations (tool, application, or workflow functions), types of data including identifiers, topics (application domains), and data formats. The applications of EDAM are within organizing tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web.

Proper citation: EDAM Ontology (RRID:SCR_006620) Copy   

•   Source: SciCrunch Registry

https://repository.niddk.nih.gov/home/

NIDDK Central Repositories are two separate contract funded components that work together to store data and samples from significant, NIDDK funded studies. First component is Biorepository that gathers, stores, and distributes biological samples from studies. Biorepository works with investigators in new and ongoing studies as realtime storage facility for archival samples.Second component is Data Repository that gathers, stores and distributes incremental or finished datasets from NIDDK funded studies Data Repository helps active data coordinating centers prepare databases and incremental datasets for archiving and for carrying out restricted queries of stored databases. Data Repository serves as Data Coordinating Center and website manager for NIDDK Central Repositories website.

Proper citation: NIDDK Central Repository (RRID:SCR_006542) Copy   

•   Source: SciCrunch Registry

https://fitbir.nih.gov/

Platform for Traumatic Brain Injury relevant data. System was developed to share data across entire TBI research field and to facilitate collaboration between laboratories and interconnectivity between informatics platforms. FITBIR implements interagency Common Data Elements for TBI research and provides tools and resources to extend data dictionary. Established submission strategy to ensure high quality and to provide maximum benefit to investigators. Qualified researchers can request access to data stored in FITBIR and/or data stored at federated repositories.

Proper citation: Federal Interagency Traumatic Brain Injury Research Informatics System (RRID:SCR_006856) Copy   

•   Source: SciCrunch Registry

http://www.ars-grin.gov/

Web server to provide germplasm information about plants, animals, microbes, invertebrates and access to databases that maintain passport, characterization, evaluation, inventory, and distribution data for the management and utilization of national germplasm collections. Under control of the U.S. Department of Agriculture's Agricultural Research Service to support the National Genetic Resources Program (NGRP). Operated by the Database Management Unit of the National Germplasm Resource Laboratory in Beltsville, Maryland.

Proper citation: Germplasm Resources Information Network (RRID:SCR_006675) Copy   

•   Source: SciCrunch Registry

http://harvard.eagle-i.net/i/0000012e-58c7-d44f-55da-381e80000000

Core to provide gene expression data analysis service. Activities range from the provision of services to fully collaborative grant funded investigations.

Proper citation: Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility (RRID:SCR_000882) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/jmosaics.html

R software that detects enriched regions of ChIP-seq data sets jointly.

Proper citation: Jmosaics (RRID:SCR_001094) Copy   

•   Source: SciCrunch Registry

http://incf.org/programs/atlasing/projects/waxholm-space

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 1st, 2023. Coordinate based reference space for the mapping and registration of neuroanatomical data. Users can download image volumes representing the canonical Waxholm Space (WHS) adult C57BL/6J mouse brain, which include T1-, T2*-, and T2-Weighted MR volumes (generated at the Duke Center for In-Vivo Microscopy), Nissl-stained optical histology (acquired at Drexel University), and a volume of labels. All volumes are represented at 21.5μ isotropic resolution. Datasets are provided as gzipped NIFTI files.

Proper citation: Waxholm Space (RRID:SCR_001592) Copy   

•   Source: SciCrunch Registry

https://github.com/vital-ai/vital-documentation/wiki/Vital-AI-Ontology

Ontology for the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. It provides a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.

Proper citation: Vital Signs Ontology (RRID:SCR_001422) Copy   

•   Source: SciCrunch Registry

http://www.farsight-toolkit.org/wiki/FARSIGHT_Toolkit

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A collection of software modules for image data handling, pre-processing, segmentation, inspection, editing, post-processing, and secondary analysis. These modules can be scripted to accomplish a variety of automated image analysis tasks. All of the modules are written in accordance with software practices of the Insight Toolkit Community. Importantly, all modules are accessible through the Python scripting language which allows users to create scripts to accomplish sophisticated associative image analysis tasks over multi-dimensional microscopy image data. This language works on most computing platforms, providing a high degree of platform independence. Another important design principle is the use of standardized XML file formats for data interchange between modules.

Proper citation: Farsight Toolkit (RRID:SCR_001728) Copy   

•   Source: SciCrunch Registry

http://surfer.nmr.mgh.harvard.edu/

Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS.

Proper citation: FreeSurfer (RRID:SCR_001847) Copy   

•   Source: SciCrunch Registry

http://amigo.geneontology.org/

Web tool to search, sort, analyze, visualize and download data of interest. Along with providing details of the ontologies, gene products and annotations, features a BLAST search, Term Enrichment and GO Slimmer tools, the GO Online SQL Environment and a user help guide.Used at the Gene Ontology (GO) website to access the data provided by the GO Consortium. Developed and maintained by the GO Consortium.

Proper citation: AmiGO (RRID:SCR_002143) Copy   

•   Source: SciCrunch Registry