CTD Chemicals (CC): Monosaccharides

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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)
Nitric oxide (NO) synthase oxygenase domain	0	Direct
Leucine zipper domain	0.00000002802	Direct
Rudiment single hybrid motif	0.00004251	Direct
PreATP-grasp domain	0.00004663	Direct
Caspase-like	0.0001522	Direct
SMAD MH1 domain	0.0001714	Direct
Carbonic anhydrase	0.0002855	Direct
LDH C-terminal domain-like	0.0002894	Direct
Flavoproteins	0.0004542	Direct
PGBD-like	0.0004908	Direct
FnI-like domain	0.0006674	Direct
Single hybrid motif	0.0006721	Direct
Glutathione synthetase ATP-binding domain-like	0.0007868	Direct
DHS-like NAD/FAD-binding domain	0.0009559	Direct
Hemopexin-like domain	0.001195	Inherited
DEATH domain	0.001306	Inherited
4-helical cytokines	0.001751	Inherited
NAD(P)-linked oxidoreductase	0.003567	Inherited
MFS general substrate transporter	0.007068	Inherited
Cyclin-like	0.05701	Inherited
Ferredoxin reductase-like, C-terminal NADP-linked domain	0.7066	Inherited
Riboflavin synthase domain-like	0.7066	Inherited
Protein kinase-like (PK-like)	0.7783	Inherited
Nuclear receptor ligand-binding domain	0.9526	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)
Nitric oxide (NO) synthase oxygenase domain	0	Direct
Leucine zipper domain	0.00000006007	Direct
NADPH-cytochrome p450 reductase FAD-binding domain-like	0.00004666	Direct
BC C-terminal domain-like	0.00004666	Direct
NADPH-cytochrome p450 reductase-like	0.00004666	Direct
Caspase catalytic domain	0.00008718	Direct
Long-chain cytokines	0.00008718	Direct
L domain	0.000102	Direct
Cytochrome p450 reductase N-terminal domain-like	0.000102	Direct
SMAD MH1 domain	0.000192	Direct
BC ATP-binding domain-like	0.000192	Direct
BC N-terminal domain-like	0.000192	Direct
SMAD domain	0.000192	Direct
LDH N-terminal domain-like	0.0003264	Direct
Lactate & malate dehydrogenases, C-terminal domain	0.0003264	Direct
Carbonic anhydrase	0.0003508	Direct
MMP N-terminal domain	0.0006056	Direct
Biotinyl/lipoyl-carrier proteins and domains	0.0007674	Direct
Fibronectin type II module	0.001095	Inherited
Hemopexin-like domain	0.001487	Inherited
Matrix metalloproteases, catalytic domain	0.001487	Inherited
Aldo-keto reductases (NADP)	0.004126	Inherited
Cyclin	0.02456	Inherited
Nuclear receptor ligand-binding domain	0.9594	Inherited
Nuclear receptor	0.9765	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)
Nitric oxide (NO) synthase oxygenase domain	0	Direct
Leucine zipper domain	0.000000012	Direct
Rudiment single hybrid motif	0.00002199	Direct
PreATP-grasp domain	0.0000242	Direct
Caspase-like	0.00008308	Direct
SMAD MH1 domain	0.00009412	Direct
Carbonic anhydrase	0.0001603	Direct
LDH C-terminal domain-like	0.0001626	Direct
Flavoproteins	0.0002605	Direct
PGBD-like	0.0002826	Direct
FnI-like domain	0.0003905	Direct
Single hybrid motif	0.0003933	Direct
Glutathione synthetase ATP-binding domain-like	0.000464	Direct
DHS-like NAD/FAD-binding domain	0.0005687	Direct
Hemopexin-like domain	0.0007202	Direct
DEATH domain	0.0007905	Direct
4-helical cytokines	0.001076	Inherited
Kringle-like	0.001282	Inherited
NAD(P)-linked oxidoreductase	0.00227	Inherited
MFS general substrate transporter	0.00467	Inherited
Cyclin-like	0.04246	Inherited
Ferredoxin reductase-like, C-terminal NADP-linked domain	0.6349	Inherited
Riboflavin synthase domain-like	0.6349	Inherited
Protein kinase-like (PK-like)	0.7082	Inherited
Nuclear receptor ligand-binding domain	0.8944	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)
57440,57440 57440 - Kringle-like 57440 - Kringle-like	0.00001459	Direct
56059,51246 56059 - Glutathione synthetase ATP-binding domain-like 51246 - Rudiment single hybrid motif	0.00002199	Direct
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain	0.00004913	Direct
47986,47986 47986 - DEATH domain 47986 - DEATH domain	0.00004913	Direct
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like	0.00004913	Direct
57889,57889 57889 - Cysteine-rich domain 57889 - Cysteine-rich domain	0.00005723	Direct
51735,56327 51735 - NAD(P)-binding Rossmann-fold domains 56327 - LDH C-terminal domain-like	0.0001626	Direct
47986,52129 47986 - DEATH domain 52129 - Caspase-like	0.0001626	Direct
47090,55486 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain	0.0002826	Direct
52440,56059 52440 - PreATP-grasp domain 56059 - Glutathione synthetase ATP-binding domain-like	0.0003933	Direct
47454,57959 47454 - A DNA-binding domain in eukaryotic transcription factors 57959 - Leucine zipper domain	0.001403	Inherited
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0.009079	Inherited
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain	0.9705	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)
52440,56059,51246 52440 - PreATP-grasp domain 56059 - Glutathione synthetase ATP-binding domain-like 51246 - Rudiment single hybrid motif	0.00002199	Direct
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like	0.00004913	Direct