CTD Chemicals (CC): Boron Compounds

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Biomedical Ontology
Like Gene Ontology (GO), biomedical ontology such as phenotype ontology classifies and organizes gene-mutant/null phenotypic information from the very general at the top to more specific terms in the directed acyclic graph (DAG) by viewing an individual term as a node and its relations to parental terms (allowing for multiple parents) as directed edges. To navigate this hierarchy, we display all parental phenotypic terms to the current phenotypic term of interest ordered by their shortest distances to the current term. Also, only direct children phenotypic terms of the current phenotypic term are listed. Biomedical ontologies we have incorporated are as follows:

Disease Ontology (DO) Ontology
DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM.
Human Phenotype (HP) Ontology
HP captures phenotypic abnormalities that are described in OMIM, along with the corresponding disease-causing genes. It includes three complementary biological concepts: Mode_of_Inheritance (MI), ONset_and_clinical_course (ON), and Phenotypic_Abnormality (PA).
Mouse Phenotype (MP) Ontology
MP describes phenotypes of the mouse after a specific gene is genetically disrupted. Using it, Mouse Genome Informatics (MGI) provides high-coverate gene-level phenotypes for the mouse.
Worm Phenotype (WP) Ontology
WP classifies and organizes phenotype descriptions for C. elegans and other nematodes. Using it, WormBase provides primary resource for phenotype annotations for C. elegans.
Yeast Phenotype (YP) Ontology
Based on YP which is the major contributor to the ‘Ascomycete phenotype ontology’, Saccharomyces Genome Database (SGD) provides single mutant phenotypes for every gene in the yeast genome.
Fly Phenotype (FP) Ontology
FP refers to FlyBase controlled vocabulary. Specifically, a structured controlled vocabulary is used for the annotation of alleles (for their mutagen etc) in FlyBase.
Fly Anatomy (FA) Ontology
FA is a structured controlled vocabulary of the anatomy of Drosophila melanogaster, used for the description of phenotypes and where a gene is expressed.
Zebrafish Anatomy (ZA) Ontology
ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
Xenopus Anatomy (XA) Ontology
XA represents the lineage of tissues and the timing of development for frogs (Xenopus laevis and Xenopus tropicalis). It is used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes.
Arabidopsis Plant Ontology (AP) Ontology
As a major contributor to Plant Ontology which describes plant anatomical and morphological structures (AN) and growth and developmental stages (DE), the Arabidopsis Information Resource (TAIR) provides arabidopsis plant ontology annotations for the model higher plant Arabidopsis thaliana.
Enzyme Commission (EC) Ontology
Each enzyme is allocated a four-digit EC number, the first three digits of which define the reaction catalysed and the fourth of which is a unique identifier (serial number). Each enzyme is also assigned a systematic name that uniquely defines the reaction catalysed.
UniProtKB KeyWords (KW) Ontology
Keywords in UniProtKB are controlled vocabulary, providing a summary of the entry content and are used to index UniProtKB/Swiss-Prot entries based on 10 categories (the category "Technical term" being excluded here). Each keyword is attributed manually to UniProtKB/Swiss-Prot entries and automatically to UniProtKB/TrEMBL entries (according to specific annotation rules).
CTD Diseases (CD) Ontology
CD is MEDIC disease vocabulary that is modified by CTD from the "Diseases" [C] branch of Medical Subject Headings (MeSH), combined with genetic disorders from the Online Mendelian Inheritance in OMIM database.
CTD Chemicals (CC) Ontology
CC is chemical vocabulary that is adapted by CTD from the "Chemicals and Drugs" category and Supplementary Concept Records of Medical Subject Headings (MeSH, a hierarchical vocabulary used to index articles for MEDLINE/PubMed).

Root: CC Hierarchy (CTD chemicals from Comparative Toxicogenomics Database)

Superfamily

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
DEATH domain	0.000000000435	Direct
Caspase-like	0.00000001025	Direct
Bcl-2 inhibitors of programmed cell death	0.000000115	Direct
Inhibitor of apoptosis (IAP) repeat	0.000000178	Direct
Nuclear receptor ligand-binding domain	0.000002845	Direct
Leucine zipper domain	0.000006847	Direct
Protein kinase-like (PK-like)	0.00001994	Direct
NAD(P)-linked oxidoreductase	0.000189	Direct
BRCT domain	0.0002042	Direct
Arginase/deacetylase	0.0005283	Direct
NAD kinase/diacylglycerol kinase-like	0.00166	Inherited
FnI-like domain	0.1034	Inherited
Family A G protein-coupled receptor-like	1	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Family

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
Caspase catalytic domain	0.00000004509	Direct
Bcl-2 inhibitors of programmed cell death	0.0000001173	Direct
Inhibitor of apoptosis (IAP) repeat	0.0000001673	Direct
Nuclear receptor	0.000001992	Direct
Nuclear receptor ligand-binding domain	0.000003512	Direct
Leucine zipper domain	0.0000085	Direct
Protein kinases, catalytic subunit	0.00005301	Direct
Aldo-keto reductases (NADP)	0.0001919	Direct
Toll/Interleukin receptor TIR domain	0.001963	Inherited
VWC domain	0.0609	Inherited
Rhodopsin-like	1	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Supra-domain (Single|Duplex|Triple)

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Supra-domain (Single)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
DEATH domain	0.0000000001767	Direct
Caspase-like	0.000000004315	Direct
Bcl-2 inhibitors of programmed cell death	0.00000005041	Direct
Inhibitor of apoptosis (IAP) repeat	0.00000007865	Direct
Nuclear receptor ligand-binding domain	0.000001347	Direct
Leucine zipper domain	0.000003326	Direct
Protein kinase-like (PK-like)	0.00001005	Direct
NAD(P)-linked oxidoreductase	0.0001042	Direct
BRCT domain	0.0001129	Direct
Arginase/deacetylase	0.0003055	Direct
Interleukin 8-like chemokines	0.0006095	Direct
SH2 domain	0.0007109	Direct
NAD kinase/diacylglycerol kinase-like	0.001018	Inherited
14-3-3 protein	0.001344	Inherited
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0.001344	Inherited
Toll/Interleukin receptor TIR domain	0.001922	Inherited
Nucleic acid-binding proteins	0.003372	Inherited
FnI-like domain	0.07965	Inherited
Family A G protein-coupled receptor-like	1	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

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Supra-domain (Duplex) in N- to C-terminal order

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0	Direct
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain	0.00000001572	Direct
47986,52129 47986 - DEATH domain 52129 - Caspase-like	0.0000003305	Direct
57184,49265 57184 - Growth factor receptor domain 49265 - Fibronectin type III	0.0002321	Direct
52113,52113 52113 - BRCT domain 52113 - BRCT domain	0.001344	Inherited
51905,55424 51905 - FAD/NAD(P)-binding domain 55424 - FAD/NAD-linked reductases, dimerisation (C-terminal) domain	0.001344	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

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Supra-domain (Triple) in N- to C-terminal order

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
57924,57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0	Direct