CTD Chemicals (CC): Fluorouracil

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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)
Inhibitor of apoptosis (IAP) repeat	0.00000002022	Direct
Cyclin-like	0.00000005273	Direct
Caspase-like	0.0000002407	Direct
ABC transporter transmembrane region	0.00002885	Direct
Bcl-2 inhibitors of programmed cell death	0.00002939	Direct
A DNA-binding domain in eukaryotic transcription factors	0.00009998	Direct
FnI-like domain	0.0001727	Direct
Purine and uridine phosphorylases	0.0003313	Direct
PurM N-terminal domain-like	0.0003313	Direct
PurM C-terminal domain-like	0.0003313	Direct
TNF receptor-like	0.0004198	Direct
GLA-domain	0.002777	Inherited
Growth factor receptor domain	0.02607	Inherited
4-helical cytokines	0.03724	Inherited
Protein kinase-like (PK-like)	0.3318	Inherited
L domain-like	0.7179	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)
Cyclin	0.00000002142	Direct
Inhibitor of apoptosis (IAP) repeat	0.00000002664	Direct
ABC transporter transmembrane region	0.000007297	Direct
Caspase catalytic domain	0.00001918	Direct
L domain	0.00001964	Direct
Bcl-2 inhibitors of programmed cell death	0.00003992	Direct
DNA replication initiator (cdc21/cdc54) N-terminal domain	0.0000684	Direct
A DNA-binding domain in eukaryotic transcription factors	0.0001365	Direct
TNF receptor-like	0.0001881	Direct
Polo-box duplicated region	0.0003508	Direct
PurM C-terminal domain-like	0.0003508	Direct
PurM N-terminal domain-like	0.0003508	Direct
Purine and uridine phosphorylases	0.0003508	Direct
Cell cycle transcription factor e2f-dp	0.000761	Direct
Growth factor receptor domain	0.001284	Inherited
GLA-domain	0.003403	Inherited
Protein kinases, catalytic subunit	0.3437	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)
Inhibitor of apoptosis (IAP) repeat	0.000000008607	Direct
Cyclin-like	0.00000002282	Direct
Caspase-like	0.0000001071	Direct
ABC transporter transmembrane region	0.00001471	Direct
Bcl-2 inhibitors of programmed cell death	0.000015	Direct
A DNA-binding domain in eukaryotic transcription factors	0.00005361	Direct
FnI-like domain	0.00009482	Direct
Purine and uridine phosphorylases	0.0001873	Direct
PurM N-terminal domain-like	0.0001873	Direct
PurM C-terminal domain-like	0.0001873	Direct
TNF receptor-like	0.0002399	Direct
NAD(P)-linked oxidoreductase	0.000801	Direct
GLA-domain	0.001746	Inherited
Growth factor receptor domain	0.01859	Inherited
4-helical cytokines	0.0271	Inherited
Protein kinase-like (PK-like)	0.2769	Inherited
L domain-like	0.6464	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
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0.0000006071	Direct
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain	0.000008318	Direct
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like	0.000008318	Direct
90123,52540 90123 - ABC transporter transmembrane region 52540 - P-loop containing nucleoside triphosphate hydrolases	0.00001471	Direct
57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like	0.00002646	Direct
47454,57959 47454 - A DNA-binding domain in eukaryotic transcription factors 57959 - Leucine zipper domain	0.00002938	Direct
47986,52129 47986 - DEATH domain 52129 - Caspase-like	0.00008113	Direct
82615,82615 82615 - Polo-box domain 82615 - Polo-box domain	0.0001873	Direct
55326,56042 55326 - PurM N-terminal domain-like 56042 - PurM C-terminal domain-like	0.0001873	Direct
57440,57440 57440 - Kringle-like 57440 - Kringle-like	0.0003634	Direct
100920,100934 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain 100934 - Heat shock protein 70kD (HSP70), C-terminal subdomain	0.0008132	Direct
57184,57603 57184 - Growth factor receptor domain 57603 - FnI-like domain	0.0008132	Direct

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
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain	0	Direct
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like	0.000008318	Direct
57586,57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like 57586 - TNF receptor-like	0.0006317	Direct
53067,100920,100934 53067 - Actin-like ATPase domain 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain 100934 - Heat shock protein 70kD (HSP70), C-terminal subdomain	0.0008132	Direct