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

A standardized terminology of dermatologic diagnoses, therapies, procedures, and laboratory tests.

Proper citation: Dermatology Lexicon (RRID:SCR_010305) Copy   

•   Source: SciCrunch Registry

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

Diagnosis ontology of clinical care classification.

Proper citation: Diagnosis Ontology of Clinical Care Classification (RRID:SCR_010306) Copy   

•   Source: SciCrunch Registry

http://www.sbg.bio.ic.ac.uk/phyre2

A structure prediction system to reliably detect remote homologies.

Proper citation: Phyre (RRID:SCR_010270) Copy   

•   Source: SciCrunch Registry

http://www.biobase-international.com

THIS RESOURCE IS OUT OF SERVICE, documented on February 1st,2022. BIOBASE offers academic and non-profit organizations free access to TRANSFAC?? non-professional version with much reduced functionality and content compared to our professional database.

Proper citation: BIOBASE Corporation (RRID:SCR_010271) Copy   

•   Source: SciCrunch Registry

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

Ontology that relates concepts and terminologies used for human nutrition in a clinical and biomedical setting.

Proper citation: Bionutrition Ontology (RRID:SCR_010272) Copy   

•   Source: SciCrunch Registry

http://toolkit.tuebingen.mpg.de/hhpred

The primary aim in developing HHpred was to provide biologists with a method for sequence database searching and structure prediction that is as easy to use as BLAST or PSI-BLAST and that is at the same time much more sensitive in finding remote homologs. In fact, HHpred''s sensitivity is competitive with the most powerful servers for structure prediction currently available. HHpred is the first server that is based on the pairwise comparison of profile hidden Markov models (HMMs). Whereas most conventional sequence search methods search sequence databases such as UniProt or the NR, HHpred searches alignment databases, like Pfam or SMART. This greatly simplifies the list of hits to a number of sequence families instead of a clutter of single sequences. All major publicly available profile and alignment databases are available through HHpred.

Proper citation: HHpred (RRID:SCR_010276) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/bitseq/

A software application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions.

Proper citation: BitSeq (RRID:SCR_009904) Copy   

•   Source: SciCrunch Registry

http://www.dol.gov/

Fosters, promotes, and develops the welfare of the wage earners, job seekers, and retirees of the United States; improves working conditions; advances opportunities for profitable employment; and assures work-related benefits and rights.

Proper citation: U.S. Department of Labor (RRID:SCR_010157) Copy   

•   Source: SciCrunch Registry

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

A top-domain ontology that provides definitions for the foundational entities of biomedicine as a basic vocabulary to unambiguously describe facts in this domain. It can furthermore serve as top-level model for creating new ontologies for more specific domains or as aid for aligning or improving existing ones.

Proper citation: BioTop Ontology (RRID:SCR_010039) Copy   

•   Source: SciCrunch Registry

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

A set of 1,437 eligibility features that were organized into a feature hierarchy using 80 breast cancer trials.

Proper citation: Eligibility Feature Hierarchy (RRID:SCR_010314) Copy   

•   Source: SciCrunch Registry

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

Ontology to describe the active components of the enzyme''s reactions (cofactors, amino acid residues and cognate ligands) and their roles in the reaction. EMO builds upon this by formalizing key concepts, and the relationships between them, necessary to define enzymes and their functions. This describes not only the general features of an enzyme, including the EC number (catalytic activity), 3D structure and cellular locations, but also allows for the detailed annotation of the mechanism. This mechanistic detail can be either at a gross level (overall reaction only), or the more detailed granularity of the steps and components required to effect the overall chemical transformation.

Proper citation: Enzyme Mechanism Ontology (RRID:SCR_010315) Copy   

•   Source: SciCrunch Registry

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

An enzyme ontology that deals with partial reactions (transformations)

Proper citation: Enzyme Reaction Ontology for partial chemical perspectives (RRID:SCR_010316) Copy   

•   Source: SciCrunch Registry

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

Ontology about the epilepsy domain and epileptic seizures. Based on the diagnosis proposed by the International League Against Epilepsy (ILAE).

Proper citation: Epilepsy Ontology (RRID:SCR_010317) Copy   

•   Source: SciCrunch Registry

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

An ontology for Loggerhead sea turtle (Caretta caretta) nesting behavior, based on the published ethogram of Hailman and Elowson. A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms.

Proper citation: Loggerhead Nesting Ontology (RRID:SCR_010318) Copy   

•   Source: SciCrunch Registry

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

Ontology to represent the set of concepts about the fire occurring in natural vegetation, its characteristics, causes and effects, with focus on Cerrado vegetation domain. The fire plays a determinant role on the structure and composition of Cerrado physiognomies.

Proper citation: Fire Ontology (RRID:SCR_010320) Copy   

•   Source: SciCrunch Registry

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

Ontology generated from the Flora Malesiana, Flora Gabon, Flora of Central Africa, and a collection of Kew''s African Floras. Every class in the ontology has at least one taxon annotation. This is the pre-classified version of the ontology; the original OWL file is at http://jagannath.pdn.cam.ac.uk/plant/flopo-unclassified.owl

Proper citation: Flora Phenotype Ontology (RRID:SCR_010321) Copy   

•   Source: SciCrunch Registry

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

OWL Representation of the models in the BioModels repository.

Proper citation: BioModels Ontology (RRID:SCR_010125) Copy   

•   Source: SciCrunch Registry

http://www.jhu.edu/

Johns Hopkins University is private research university in Baltimore, Maryland. Founded in 1876, university was named for its first benefactor, American entrepreneur, abolitionist, and philanthropist Johns Hopkins.

Proper citation: Johns Hopkins University; Maryland; USA (RRID:SCR_010247) Copy   

•   Source: SciCrunch Registry

http://bioportal.bioontology.org/ontologies/ASDPTO

Ontology that encapsulates the Autism Spectrum Disorder behavioral phenotype, informed by the standard ASD assessment instruments and the currently known characteristics of this disorder.

Proper citation: Autism Spectrum Disorder Phenotype Ontology (RRID:SCR_010006) Copy   

•   Source: SciCrunch Registry

http://bioinf.cs.ucl.ac.uk

Group headed by Professor David Jones, and was originally founded as the Joint Research Council funded Bioinformatics Unit within the Department of Computer Science at University College London. Supports the following tools: Protein Structure Prediction Threading (THREADER) Ab initio folding simulations Secondary structure prediction (PSIPRED) Protein disorder prediction (DISOPRED) Protein domain prediction (DomPred) Database of protein disorder (DisoDB) Protein Sequence Analysis Protein function prediction (ffpred) Metsite: Metal binding residue prediction HSPred : Protein-protein interaction characterisation Amino acid substitution matrices Hidden Markov Models (collaboration with N. Goldman, Cambridge, & J. Thorne, NCSU) Genome Analysis Genomic fold recognition (GenTHREADER) Genome annotation using software agents Protein Structure Classification CATH (collaboration with J. Thornton & C. Orengo, UCL Biochemistry) Transmembrane Protein Modelling MEMSAT & MEMSATSVM Folding In Lipid Membranes (FILM) MEMPACK Biological Applications of Data-mining and Machine Learning Techniques Information extraction for biological research (BioRat) Microarray Analysis Data integration for microarray analysis Data visualization Systems Biology Systems biology applied to stem cells Legacy Services (to be retired shortly) Comparison of structure classifications (CATH/SCOP/FSSP) Genomic Threading Database (GTD)

Proper citation: UCL Bioinformatics Group (RRID:SCR_010248) Copy   

•   Source: SciCrunch Registry