CTD Chemicals (CC): Benzodioxoles

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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)
Protein kinase-like (PK-like)	0.00000000404	Direct
Cytochrome P450	0.000000006009	Direct
Caspase-like	0.0000004827	Direct
Bcl-2 inhibitors of programmed cell death	0.00002737	Direct
PGBD-like	0.0000683	Direct
p53-like transcription factors	0.0001139	Direct
Hemopexin-like domain	0.0001439	Direct
4-helical cytokines	0.0002711	Direct
Leucine zipper domain	0.0002821	Direct
E set domains	0.005319	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)
Cytochrome P450	0.0000000141	Direct
Protein kinases, catalytic subunit	0.0000002441	Direct
Caspase catalytic domain	0.0000003158	Direct
Rel/Dorsal transcription factors, DNA-binding domain	0.000008592	Direct
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.00002725	Direct
Bcl-2 inhibitors of programmed cell death	0.00003733	Direct
MMP N-terminal domain	0.00009408	Direct
Hemopexin-like domain	0.0001997	Direct
Matrix metalloproteases, catalytic domain	0.0001997	Direct
Leucine zipper domain	0.0004497	Direct

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)
Protein kinase-like (PK-like)	0.000000001678	Direct
Cytochrome P450	0.000000002511	Direct
Caspase-like	0.000000218	Direct
Bcl-2 inhibitors of programmed cell death	0.00001393	Direct
PGBD-like	0.00003601	Direct
p53-like transcription factors	0.00006135	Direct
Hemopexin-like domain	0.00007839	Direct
4-helical cytokines	0.0001518	Direct
Leucine zipper domain	0.0001583	Direct
Metalloproteases ("zincins"), catalytic domain	0.002394	Inherited
E set domains	0.003455	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)
49417,81296 49417 - p53-like transcription factors 81296 - E set domains	0.000003095	Direct
47090,55486 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain	0.00003601	Direct
48371,48371 48371 - ARM repeat 48371 - ARM repeat	0.000838	Direct