CTD Chemicals (CC): Oximes

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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)
Cytochrome P450	0.000000000009282	Direct
4-helical cytokines	0.00000000007901	Direct
Nuclear receptor ligand-binding domain	0.00000003004	Direct
Thiolase-like	0.00000003334	Direct
Terpenoid synthases	0.00001938	Direct
ABC transporter transmembrane region	0.0000197	Direct
Interleukin 8-like chemokines	0.00002092	Direct
Thioesterase/thiol ester dehydrase-isomerase	0.0000583	Direct
alpha/beta-Hydrolases	0.0002795	Direct
FabD/lysophospholipase-like	0.0006334	Direct
Heat shock protein 70kD (HSP70), peptide-binding domain	0.001455	Inherited
ClpP/crotonase	0.002238	Inherited
Glycerol-3-phosphate (1)-acyltransferase	0.002238	Inherited
Toll/Interleukin receptor TIR domain	0.002446	Inherited
Acetyl-CoA synthetase-like	0.004019	Inherited
Actin-like ATPase domain	0.008951	Inherited
Protein kinase-like (PK-like)	0.1523	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	0.0000000002319	Direct
Nuclear receptor ligand-binding domain	0.00000003637	Direct
Short-chain cytokines	0.0000001996	Direct
Nuclear receptor	0.0000003111	Direct
Thiolase-related	0.000004701	Direct
ABC transporter transmembrane region	0.00001024	Direct
Interleukin 8-like chemokines	0.00002136	Direct
Long-chain cytokines	0.0004546	Direct
Heat shock protein 70kD (HSP70), peptide-binding domain	0.0008371	Direct
ABC transporter ATPase domain-like	0.001198	Inherited
Actin/HSP70	0.001564	Inherited
Toll/Interleukin receptor TIR domain	0.001886	Inherited
Acetyl-CoA synthetase-like	0.00416	Inherited
Protein kinases, catalytic subunit	0.1101	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)
Cytochrome P450	0.000000000003665	Direct
4-helical cytokines	0.00000000003159	Direct
Nuclear receptor ligand-binding domain	0.00000001288	Direct
Thiolase-like	0.00000001432	Direct
Terpenoid synthases	0.000009754	Direct
ABC transporter transmembrane region	0.000009919	Direct
Interleukin 8-like chemokines	0.00001055	Direct
Thioesterase/thiol ester dehydrase-isomerase	0.00003053	Direct
alpha/beta-Hydrolases	0.0001568	Direct
FabD/lysophospholipase-like	0.0003695	Direct
Glucocorticoid receptor-like (DNA-binding domain)	0.0006933	Direct
Bcl-2 inhibitors of programmed cell death	0.0008855	Direct
Caspase-like	0.0008855	Direct
Heat shock protein 70kD (HSP70), peptide-binding domain	0.0008855	Direct
PYP-like sensor domain (PAS domain)	0.0009239	Direct
ClpP/crotonase	0.001392	Inherited
Glycerol-3-phosphate (1)-acyltransferase	0.001392	Inherited
Toll/Interleukin receptor TIR domain	0.001527	Inherited
Acetyl-CoA synthetase-like	0.002577	Inherited
Actin-like ATPase domain	0.005994	Inherited
Protein kinase-like (PK-like)	0.1199	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)
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain	0.0000002183	Direct
53901,53901 53901 - Thiolase-like 53901 - Thiolase-like	0.0000003783	Direct
54637,54637 54637 - Thioesterase/thiol ester dehydrase-isomerase 54637 - Thioesterase/thiol ester dehydrase-isomerase	0.0000008291	Direct
90123,52540 90123 - ABC transporter transmembrane region 52540 - P-loop containing nucleoside triphosphate hydrolases	0.000009919	Direct
52540,90123 52540 - P-loop containing nucleoside triphosphate hydrolases 90123 - ABC transporter transmembrane region	0.00001875	Direct
53067,100920 53067 - Actin-like ATPase domain 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain	0.0008855	Direct
53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain	0.003452	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)
52540,90123,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 90123 - ABC transporter transmembrane region 52540 - P-loop containing nucleoside triphosphate hydrolases	0.00001875	Direct
90123,52540,90123 90123 - ABC transporter transmembrane region 52540 - P-loop containing nucleoside triphosphate hydrolases 90123 - ABC transporter transmembrane region	0.00001875	Direct
53067,53067,100920 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain	0.0008855	Direct