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http://www.youtube.com/user/NIGMS/

YouTube videos provided by the National Institute of General Medical Sciences (NIGMS).

Proper citation: NIGMS - YouTube (RRID:SCR_005678) Copy   

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http://pidfinder.appspot.com/

PIDFinder is a tool for the exploration of the Primary Immunodeficiency Disease Ontology. Apart from browsing the knowledge contained in the ontology, it can also be used for the identification of PIDs based on a set of observed Phenotypes. The PidFinder web application is a developing prototype application that allows non-bioinformaticians to quickly view and use the knowledge contained in the Primary Immunodeficiency Disease Ontology. The application consists of a number of components: * The PIDFinder: allows the selection of a set of phenotypes and subsequently compares the set with the canonical set of phenotypes defined in the PID Ontology. The phenotypes, that can be selected are grouped by biomarker and are thus available in a number of different facets. Once phenotypes have been selected, the application compares them to canonical phenotypes associated with PIDs in the PID Ontology, by computing a semantic similarity measure. The similarity is determined using a Tanimoto Distance - the more closely related an observed phenotype is to a canonical ontology phenotype, the closer the calculated Tanimoto Distance is to 1 - with increasing dissimilarity, the Tanimoto Coefficient tends towards 0. * The Phenotype Explorer: a rudimentary browser for phenotypes currently contained in the PID Ontology. The browser allows the user to find phenotypes based on biomarker categories and provides some basic definitions (not all definitions are available at this stage) and disease association information. * A Heatmap comparing the phenotypic overlap of PIDs: In essence, the heatmap is a many-to-many comparison of the phenotypic overlap between all Primary Immunodeficiency Diseases contained in the PID Ontology. Again, overlap is calculated using a Tanimoto Distance. The heatmap is a matrix, plotting the Tanimoto coefficients for every PID/PID pair. Increased off-diagonal overlap between PIDs most likely indicates genes in the same pathway. * A Phenotype Frequency Visualization: The phenotype frequency visualization is a simple bar chart indicating how often a particular phenotype is associated with a Primary Immunodeficiency Disease in the Ontology. * A PID Expert map: All of the phenotypes and knowledge contained in the Primary Immunodeficiency Disease Ontology has been extracted from primary clinical or research literature. To construct the map, we have extracted the affiliations and locations of the authors of the literature sources and overlayed them on a map. The hope is that this will facilitate the identification of (local) experts on primary immunodeficiency diseases.

Proper citation: PIDFinder (RRID:SCR_005833) Copy   

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http://tolweb.org/tree/

A collection of information about biodiversity compiled collaboratively by hundreds of expert and amateur contributors. Its goal is to contain a page with pictures, text, and other information for every species and for each group of organisms, living or extinct. Connections between Tree of Life web pages follow phylogenetic branching patterns between groups of organisms, so visitors can browse the hierarchy of life and learn about phylogeny and evolution as well as the characteristics of individual groups.

Proper citation: Tree of Life Web Project (RRID:SCR_005673) Copy   

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http://www.snpedia.com/index.php/SNPedia

Wiki investigating human genetics including information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain your DNA. It is based on a wiki model in order to foster communication about genetic variation and to allow interested community members to help it evolve to become ever more relevant. As the cost of genotyping (and especially of fully determining your own genomic sequence) continues to drop, we''''ll all want to know more - a lot more - about the meaning of these DNA variations and SNPedia will be here to help. SNPedia has been launched to help realize the potential of the Human Genome Project to connect to our daily lives and well-being. For more information see the Wikipedia page, http://en.wikipedia.org/wiki/SNPedia * Download URL: http://www.SNPedia.com/index.php/Bulk * Web Service URL: http://bots.SNPedia.com/api.php

Proper citation: SNPedia (RRID:SCR_006125) Copy   

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http://www.compbio.dundee.ac.uk/gotcha/gotcha.php

GOtcha provides a prediction of a set of GO terms that can be associated with a given query sequence. Each term is scored independently and the scores calibrated against reference searches to give an accurate percentage likelihood of correctness. These results can be displayed graphically. Why is GOtcha different to what is already out there and why should you be using it? * GOtcha uses a method where it combines information from many search hits, up to and including E-values that are normally discarded. This gives much better sensitivity than other methods. * GOtcha provides a score for each individual term, not just the leaf term or branch. This allows the discrimination between confident assignments that one would find at a more general level and the more specific terms that one would have lower confidence in. * The scores GOtcha provides are calibrated to give a real estimate of correctness. This is expressed as a percentage, giving a result that non-experts are comfortable in interpreting. * GOtcha provides graphical output that gives an overview of the confidence in, or potential alternatives for, particular GO term assignments. The tool is currently web-based; contact David Martin for details of the standalone version. Platform: Online tool

Proper citation: GOtcha (RRID:SCR_005790) Copy   

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http://cossmos.slu.edu/

Database to search through the nucleic acid structures from the Protein Data Bank and examine structural motifs, including (a)symmetric internal loops, bulge loops, and hairpin loops. They have compiled over 2,000 three-dimensional structures, which can now be searched using different parameters, including PDB information, experimental technique, sequence, and motif type. RNA secondary structure is important for designing therapeutics, understanding protein-RNA binding and predicting tertiary structure of RNA. Several databases and downloadable programs exist that specialize in the three-dimensional (3D) structure of RNA, but none focus specifically on secondary structural motifs such as internal, bulge and hairpin loops. To create the RNA CoSSMos database, 2156 Protein Data Bank (PDB) files were searched for internal, bulge and hairpin loops, and each loop''''s structural information, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions, was included in the database. False positives were defined, identified and reclassified or omitted from the database to ensure the most accurate results possible. Users can search via general PDB information, experimental parameters, sequence and specific motif and by specific structural parameters in the subquery page after the initial search. Returned results for each search can be viewed individually or a complete set can be downloaded into a spreadsheet to allow for easy comparison. The RNA CoSSMos database is updated weekly.

Proper citation: RNA CoSSMos (RRID:SCR_006120) Copy   

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http://xldb.fc.ul.pt/biotools/rebil/goa/

A tool for assisting the GO annotation of UniProt entries by linking the GO terms present in the uncurated annotations with evidence text automatically extracted from the documents linked to UniProt entries. Platform: Online tool

Proper citation: GoAnnotator (RRID:SCR_005792) Copy   

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https://data.4tu.nl/portal

International data repository for science, engineering and design. Services include curation, sharing, long-term access and preservation of research datasets. These services are available to anyone around the world. In addition, 4TU.ResearchData also offers training and resources to researchers to support them in making research data findable, accessible, interoperable and reproducible (FAIR).

Proper citation: 4TU.ResearchData (RRID:SCR_023125) Copy   

•   Source: SciCrunch Registry
  

https://github.com/im3sanger/dndscv

Software R package is group of maximum likelihood dN/dS methods designed to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole-exome level.Used to detect cancer driver genes on datasets ranging from few samples to thousands of samples, in whole-exome/genome or targeted sequencing studies.

Proper citation: dNdScv (RRID:SCR_023123) Copy   

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https://github.com/AlexandrovLab/SigProfilerExtractor/

Software tool for de novo extraction of mutational signatures from data generated in matrix format. Identifies number of operative mutational signatures, their activities in each sample, and probability for each signature to cause specific mutation type in cancer sample.

Proper citation: SigProfilerExtractor (RRID:SCR_023121) Copy   

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http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/AnneOTate.cgi

Web search tool to gain overview of set of articles retrieved by PubMed query. Used to support user driven summarization, drill down and browsing of PubMed search results. Value-added PubMed search engine for analysis and text mining.

Proper citation: Anne O'Tate (RRID:SCR_023086) Copy   

•   Source: SciCrunch Registry
  

https://s-risk.be/en

Web tool for assessing exposure and human health risks at contaminated sites. Fate and distribution of chemical pollutants in soil are calculated according to steady-state conservation of mass principles.Risks are calculated by comparing exposures with toxicological reference values and concentrations with toxicological or legal reference concentrations.

Proper citation: S-Risk (RRID:SCR_023085) Copy   

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http://purl.bioontology.org/ontology/ADW

An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.

Proper citation: Animal Natural History and Life History Ontology (RRID:SCR_010292) Copy   

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http://purl.bioontology.org/ontology/COSTART

Ontology for coding, filing, and retrieving post-marketing adverse drug and biologic experience reports. It is organized in body system and pathophysiology hierarchies, as well as a separate fetal/neonatal category of less than 20 terms. COSTART has been superseded by the Medical Dictionary for Regulatory Activities (MedDRA) Terminology. For more information about MedDRA in the Metathesaurus, see the MedDRA source synopsis. COSTART was last updated in the Metathesaurus in 1999.

Proper citation: Coding Symbols for a Thesaurus of Adverse Reaction Terms (RRID:SCR_010294) Copy   

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http://purl.bioontology.org/ontology/NCBITAXON

Ontology that is an automatic translation of the NCBI taxonomy (a taxonomic classification of living organisms and associated artifacts) database into obo/owl.

Proper citation: NCBITaxon (RRID:SCR_000479) Copy   

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http://www.bioconductor.org/packages/2.14/bioc/html/GLAD.html

Software for analysis of array CGH data: detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.

Proper citation: GLAD (RRID:SCR_001284) Copy   

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https://bioconductor.org/packages/DEP/

Software R package provides integrated analysis workflow for analysis of mass spectrometry proteomics data for differential protein expression or differential enrichment.

Proper citation: Differential Enrichment analysis of Proteomics data (RRID:SCR_023090) Copy   

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http://purl.bioontology.org/ontology/HC

An ontology for courtship behavior of the spider Habronattus californicus. A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms.

Proper citation: Habronattus Courtship Ontology (RRID:SCR_010334) Copy   

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https://portal.aodn.org.au/

Interoperable online network of marine and climate data resources.AODN Portal provides access to all available Australian marine and climate science data and provides the primary access to IMOS data.

Proper citation: Australian Ocean Data Network (RRID:SCR_023134) Copy   

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https://ahed.nasa.gov

Astrobiology Habitable Environments Database (AHED) is a new data system being developed as a long-term, open-access repository for astrobiology data. AHED is intended to store user-contributed results from NASA or externally-funded research in astrobiology, and to encourage sharing and synergy within the astrobiology community.

Proper citation: Astrobiology Habitable Environments Database (RRID:SCR_023133) Copy   

•   Source: SciCrunch Registry