Disease Ontology (DO): carcinoma

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)
Purine and uridine phosphorylases	0	Direct
FAS1 domain	0	Direct
Synuclein	0	Direct
Nuclear receptor coactivator interlocking domain	0	Direct
HSP90 C-terminal domain	0	Direct
Lesion bypass DNA polymerase (Y-family), little finger domain	0	Direct
p53 tetramerization domain	0	Direct
Insulin-like	0	Direct
PGBD-like	0.000001601	Direct
Hemopexin-like domain	0.00004304	Direct
Bcl-2 inhibitors of programmed cell death	0.0002382	Direct
Intermediate filament protein, coiled coil region	0.128	Inherited
Prefoldin	0.2805	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)
p53 DNA-binding domain-like	0	Direct
Synuclein	0	Direct
Retinoblastoma tumor suppressor domains	0	Direct
L domain	0	Direct
Insulin-like	0	Direct
HSP90 C-terminal domain	0	Direct
FAS1 domain	0	Direct
p53 tetramerization domain	0	Direct
Purine and uridine phosphorylases	0	Direct
Gelsolin-like	0	Direct
Uteroglobin-like	0	Direct
Lesion bypass DNA polymerase (Y-family), catalytic domain	0	Direct
Heat shock protein 90, HSP90, N-terminal domain	0	Direct
Hsp90 middle domain	0	Direct
Nuclear receptor coactivator interlocking domain	0	Direct
PAS domain of steroid receptor coactivator 1A, NCo-A1	0	Direct
Matrix metalloproteases, catalytic domain	0.0000009943	Direct
MMP N-terminal domain	0.000001312	Direct
Ephrin receptor ligand binding domain	0.00001017	Direct
Hemopexin-like domain	0.00003742	Direct
Bcl-2 inhibitors of programmed cell death	0.0001877	Direct
Platelet-derived growth factor-like	0.0006213	Direct
Hexokinase	0.02782	Inherited
C5 cytosine-specific DNA methylase, DCM	0.02782	Inherited
Intermediate filament protein, coiled coil region	0.1091	Inherited
Protein kinase cysteine-rich domain (cys2, phorbol-binding domain)	0.1779	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)
Nuclear receptor coactivator interlocking domain	0	Direct
Lesion bypass DNA polymerase (Y-family), little finger domain	0	Direct
p53 tetramerization domain	0	Direct
Purine and uridine phosphorylases	0	Direct
Insulin-like	0	Direct
Synuclein	0	Direct
FAS1 domain	0	Direct
HSP90 C-terminal domain	0	Direct
PGBD-like	0.0000008335	Direct
Hemopexin-like domain	0.00002474	Direct
Bcl-2 inhibitors of programmed cell death	0.0001432	Direct
Serine protease inhibitors	0.02561	Inherited
DNA-glycosylase	0.02561	Inherited
Intermediate filament protein, coiled coil region	0.1028	Inherited
Prefoldin	0.2374	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)
49417,47719 49417 - p53-like transcription factors 47719 - p53 tetramerization domain	0	Direct
49562,57889 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 57889 - Cysteine-rich domain	0	Direct
57184,49265 57184 - Growth factor receptor domain 49265 - Fibronectin type III	0	Direct
82153,82153 82153 - FAS1 domain 82153 - FAS1 domain	0	Direct
57196,90193 57196 - EGF/Laminin 90193 - Notch domain	0	Direct
57603,82895 57603 - FnI-like domain 82895 - TSP-1 type 1 repeat	0	Direct
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain	0	Direct
56672,100879 56672 - DNA/RNA polymerases 100879 - Lesion bypass DNA polymerase (Y-family), little finger domain	0	Direct
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like	0	Direct
57184,57603 57184 - Growth factor receptor domain 57603 - FnI-like domain	0	Direct
55753,55753 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins	0	Direct
54236,57889 54236 - Ubiquitin-like 57889 - Cysteine-rich domain	0	Direct
57302,57302 57302 - Snake toxin-like 57302 - Snake toxin-like	0	Direct
90193,90193 90193 - Notch domain 90193 - Notch domain	0	Direct
47090,55486 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain	0.0000008335	Direct
56112,47769 56112 - Protein kinase-like (PK-like) 47769 - SAM/Pointed domain	0.00000718	Direct
55486,50923 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain	0.00003445	Direct
49785,57184 49785 - Galactose-binding domain-like 57184 - Growth factor receptor domain	0.00006316	Direct
46579,64593 46579 - Prefoldin 64593 - Intermediate filament protein, coiled coil region	0.005982	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)
52058,48726,48726 52058 - L domain-like 48726 - Immunoglobulin 48726 - Immunoglobulin	0	Direct
57196,57196,90193 57196 - EGF/Laminin 57196 - EGF/Laminin 90193 - Notch domain	0	Direct
53067,53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain	0	Direct
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain	0	Direct
49562,57889,57889 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 57889 - Cysteine-rich domain 57889 - Cysteine-rich domain	0	Direct
55753,55753,55753 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins	0	Direct
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like	0	Direct
49785,57184,49265 49785 - Galactose-binding domain-like 57184 - Growth factor receptor domain 49265 - Fibronectin type III	0	Direct
47090,55486,50923 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain	0.00001974	Direct