CTD Chemicals (CC): Organophosphonates

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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)
PHM/PNGase F	0	Direct
Caspase-like	0.0000000003363	Direct
TNF receptor-like	0.0000007493	Direct
DEATH domain	0.000003782	Direct
EGF/Laminin	0.0001512	Direct
Bcl-2 inhibitors of programmed cell death	0.0001562	Direct
Serum albumin-like	0.0005256	Direct
Interleukin 8-like chemokines	0.0005733	Direct
Inhibitor of apoptosis (IAP) repeat	0.0005787	Direct
MFS general substrate transporter	0.0009911	Direct
Tubulin C-terminal domain-like	0.00436	Inherited
Tubulin nucleotide-binding domain-like	0.00436	Inherited
Flavoproteins	0.006854	Inherited
Immunoglobulin	0.008095	Inherited
Periplasmic binding protein-like I	0.02672	Inherited
Fibronectin type III	0.03561	Inherited
Nuclear receptor ligand-binding domain	0.0425	Inherited
S15/NS1 RNA-binding domain	0.0441	Inherited
Lipocalins	0.09422	Inherited
Neurotransmitter-gated ion-channel transmembrane pore	0.2488	Inherited
Nicotinic receptor ligand binding domain-like	0.2488	Inherited
Nucleotidylyl transferase	0.2548	Inherited
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.3252	Inherited
Class II aaRS and biotin synthetases	0.3613	Inherited
alpha/beta-Hydrolases	0.3763	Inherited
Glucocorticoid receptor-like (DNA-binding domain)	0.4606	Inherited
Class II aaRS ABD-related	0.5667	Inherited
P-loop containing nucleoside triphosphate hydrolases	0.7703	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)
Peptidylglycine alpha-hydroxylating monooxygenase, PHM	0	Direct
Variant SAM domain	0	Direct
Caspase catalytic domain	0.0000000146	Direct
TNF receptor-like	0.0000008548	Direct
Bcl-2 inhibitors of programmed cell death	0.0001638	Direct
Serum albumin-like	0.0004998	Direct
Inhibitor of apoptosis (IAP) repeat	0.0005747	Direct
Interleukin 8-like chemokines	0.0007448	Direct
Caspase recruitment domain, CARD	0.0009121	Direct
DEATH effector domain, DED	0.002815	Inherited
Tubulin, GTPase domain	0.004851	Inherited
Tubulin, C-terminal domain	0.004851	Inherited
a tRNA synthase domain	0.01044	Inherited
G proteins	0.0148	Inherited
C1 set domains (antibody constant domain-like)	0.02039	Inherited
Variant RING domain	0.03508	Inherited
Laminin-type module	0.03576	Inherited
Nuclear receptor	0.03689	Inherited
Class I aminoacyl-tRNA synthetases (RS), catalytic domain	0.04349	Inherited
Nuclear receptor ligand-binding domain	0.04925	Inherited
Higher-molecular-weight phosphotyrosine protein phosphatases	0.1696	Inherited
Glutathione S-transferase (GST), N-terminal domain	0.2042	Inherited
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.241	Inherited
Nicotinic receptor ligand binding domain-like	0.2437	Inherited
Neurotransmitter-gated ion-channel transmembrane pore	0.2646	Inherited
Fatty acid binding protein-like	0.2759	Inherited
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	0.3006	Inherited
Glutathione S-transferase (GST), C-terminal domain	0.3778	Inherited
Anticodon-binding domain of Class II aaRS	0.3796	Inherited
Acetylcholinesterase-like	0.4865	Inherited
Homeodomain	0.9878	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)
PHM/PNGase F	0	Direct
Caspase-like	0.0000000001362	Direct
TNF receptor-like	0.0000003426	Direct
DEATH domain	0.000001804	Direct
EGF/Laminin	0.00008252	Direct
Bcl-2 inhibitors of programmed cell death	0.00008539	Direct
Serum albumin-like	0.0003038	Direct
Interleukin 8-like chemokines	0.0003327	Direct
Inhibitor of apoptosis (IAP) repeat	0.0003361	Direct
MFS general substrate transporter	0.000591	Direct
Tubulin nucleotide-binding domain-like	0.002806	Inherited
Tubulin C-terminal domain-like	0.002806	Inherited
Flavoproteins	0.004522	Inherited
Immunoglobulin	0.005394	Inherited
Periplasmic binding protein-like I	0.01908	Inherited
Fibronectin type III	0.02585	Inherited
Periplasmic binding protein-like II	0.02843	Inherited
Nuclear receptor ligand-binding domain	0.03116	Inherited
S15/NS1 RNA-binding domain	0.0324	Inherited
Lipocalins	0.07219	Inherited
GST C-terminal domain-like	0.1989	Inherited
Nicotinic receptor ligand binding domain-like	0.203	Inherited
Neurotransmitter-gated ion-channel transmembrane pore	0.203	Inherited
Nucleotidylyl transferase	0.2082	Inherited
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	0.271	Inherited
Class II aaRS and biotin synthetases	0.3038	Inherited
alpha/beta-Hydrolases	0.3173	Inherited
Glucocorticoid receptor-like (DNA-binding domain)	0.3952	Inherited
Class II aaRS ABD-related	0.496	Inherited
PLP-dependent transferases	0.5724	Inherited
P-loop containing nucleoside triphosphate hydrolases	0.6999	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)
49742,49742 49742 - PHM/PNGase F 49742 - PHM/PNGase F	0	Direct
48350,55961 48350 - GTPase activation domain, GAP 55961 - Bet v1-like	0	Direct
57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0	Direct
57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like	0.0000000001366	Direct
47986,52129 47986 - DEATH domain 52129 - Caspase-like	0.0000001597	Direct
48552,48552 48552 - Serum albumin-like 48552 - Serum albumin-like	0.0003038	Direct
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.0007284	Direct
57716,48508 57716 - Glucocorticoid receptor-like (DNA-binding domain) 48508 - Nuclear receptor ligand-binding domain	0.002372	Inherited
52490,55307 52490 - Tubulin nucleotide-binding domain-like 55307 - Tubulin C-terminal domain-like	0.002806	Inherited
103473,103473 103473 - MFS general substrate transporter 103473 - MFS general substrate transporter	0.01744	Inherited
52799,52799 52799 - (Phosphotyrosine protein) phosphatases II 52799 - (Phosphotyrosine protein) phosphatases II	0.06876	Inherited
63712,90112 63712 - Nicotinic receptor ligand binding domain-like 90112 - Neurotransmitter-gated ion-channel transmembrane pore	0.203	Inherited
52833,47616 52833 - Thioredoxin-like 47616 - GST C-terminal domain-like	0.2594	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)
50729,50729,48350 50729 - PH domain-like 50729 - PH domain-like 48350 - GTPase activation domain, GAP	0	Direct
50729,50729,57863 50729 - PH domain-like 50729 - PH domain-like 57863 - ArfGap/RecO-like zinc finger	0	Direct
57924,57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0	Direct
57586,57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like 57586 - TNF receptor-like	0.000889	Direct
48552,48552,48552 48552 - Serum albumin-like 48552 - Serum albumin-like 48552 - Serum albumin-like	0.001884	Inherited
50729,55550,56112 50729 - PH domain-like 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.001884	Inherited
55550,56112,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) 56112 - Protein kinase-like (PK-like)	0.001884	Inherited