CTD Chemicals (CC): Oligonucleotides

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).

Superfamily

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Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
Uracil-DNA glycosylase-like	0	Direct
BRCT domain	0.00000000002403	Direct
Domain of poly(ADP-ribose) polymerase	0.0000001884	Direct
post-AAA+ oligomerization domain-like	0.00000251	Direct
DNA/RNA polymerases	0.000006969	Direct
Cyclin-like	0.00005488	Direct
PIN domain-like	0.00009097	Direct
ADP-ribosylation	0.0009863	Direct
SMAD/FHA domain	0.4494	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)
DNA polymerase I	0.00000003783	Direct
Domain of poly(ADP-ribose) polymerase	0.0000001559	Direct
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.00000442	Direct
Poly(ADP-ribose) polymerase, C-terminal domain	0.000004808	Direct
RecA protein-like (ATPase-domain)	0.0001115	Direct
Cyclin	0.0001307	Direct
FHA domain	0.0001307	Direct
Extended AAA-ATPase domain	0.001203	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)
Uracil-DNA glycosylase-like	0	Direct
BRCT domain	0.000000000009534	Direct
Domain of poly(ADP-ribose) polymerase	0.00000008341	Direct
post-AAA+ oligomerization domain-like	0.000001184	Direct
DNA/RNA polymerases	0.000003387	Direct
Cyclin-like	0.00002869	Direct
PIN domain-like	0.00004859	Direct
ADP-ribosylation	0.0005879	Direct
Ribonuclease H-like	0.003063	Inherited
SMAD/FHA domain	0.3851	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)
53098,56672 53098 - Ribonuclease H-like 56672 - DNA/RNA polymerases	0.00000008341	Direct
47587,56399 47587 - Domain of poly(ADP-ribose) polymerase 56399 - ADP-ribosylation	0.00000008341	Direct
52540,48019 52540 - P-loop containing nucleoside triphosphate hydrolases 48019 - post-AAA+ oligomerization domain-like	0.000001184	Direct
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0.00003578	Direct