Disease Ontology (DO): cell type cancer

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)
p53 tetramerization domain	0	Direct
Di-copper centre-containing domain	0	Direct
Synuclein	0	Direct
Nuclear receptor coactivator interlocking domain	0	Direct
Lesion bypass DNA polymerase (Y-family), little finger domain	0	Direct
HSP90 C-terminal domain	0	Direct
Integrin beta tail domain	0	Direct
Insulin-like	0	Direct
Purine and uridine phosphorylases	0	Direct
FAS1 domain	0	Direct
PGBD-like	0.0004998	Direct
Metalloproteases ("zincins"), catalytic domain	0.0005481	Direct
Hemopexin-like domain	0.00183	Inherited
Growth factor receptor domain	0.004444	Inherited
Bcl-2 inhibitors of programmed cell death	0.006546	Inherited
Protein kinase-like (PK-like)	0.04215	Inherited
Caspase-like	0.06396	Inherited
Intermediate filament protein, coiled coil region	0.06978	Inherited
Prefoldin	0.5469	Inherited
Ubiquitin-like	0.5555	Inherited
Thioredoxin-like	0.6005	Inherited
Ran binding protein zinc finger-like	0.8455	Inherited
HMG-box	0.9009	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)
Integrin beta tail domain	0	Direct
HSP90 C-terminal domain	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
DEATH effector domain, DED	0	Direct
Neurotrophin	0	Direct
Integrin beta EGF-like domains	0	Direct
Uteroglobin-like	0	Direct
Tissue inhibitor of metalloproteinases, TIMP	0	Direct
PAS domain of steroid receptor coactivator 1A, NCo-A1	0	Direct
Insulin-like	0	Direct
Purine and uridine phosphorylases	0	Direct
Gelsolin-like	0	Direct
L domain	0	Direct
Synuclein	0	Direct
p53 DNA-binding domain-like	0	Direct
p53 tetramerization domain	0	Direct
Nuclear receptor coactivator interlocking domain	0	Direct
FAS1 domain	0	Direct
Transferrin	0	Direct
Retinoblastoma tumor suppressor domains	0	Direct
S100 proteins	0.00005537	Direct
MMP N-terminal domain	0.0003793	Direct
Growth factor receptor domain	0.0004214	Direct
Matrix metalloproteases, catalytic domain	0.0008824	Direct
Hemopexin-like domain	0.001417	Inherited
Ephrin receptor ligand binding domain	0.003064	Inherited
Bcl-2 inhibitors of programmed cell death	0.005064	Inherited
Platelet-derived growth factor-like	0.02213	Inherited
Caspase catalytic domain	0.03269	Inherited
Hexokinase	0.04575	Inherited
Intermediate filament protein, coiled coil region	0.06599	Inherited
Protein kinases, catalytic subunit	0.07784	Inherited
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.1144	Inherited
Protein kinase cysteine-rich domain (cys2, phorbol-binding domain)	0.1158	Inherited
C5 cytosine-specific DNA methylase, DCM	0.1596	Inherited
Ras-binding domain, RBD	0.2432	Inherited
Ran binding protein zinc finger-like	0.8246	Inherited
HMG-box	0.8859	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)
p53 tetramerization domain	0	Direct
Purine and uridine phosphorylases	0	Direct
HSP90 C-terminal domain	0	Direct
Synuclein	0	Direct
Di-copper centre-containing domain	0	Direct
FAS1 domain	0	Direct
Insulin-like	0	Direct
Nuclear receptor coactivator interlocking domain	0	Direct
Integrin beta tail domain	0	Direct
Lesion bypass DNA polymerase (Y-family), little finger domain	0	Direct
PGBD-like	0.0003056	Direct
Metalloproteases ("zincins"), catalytic domain	0.0003365	Direct
Hemopexin-like domain	0.00118	Inherited
Growth factor receptor domain	0.002997	Inherited
Bcl-2 inhibitors of programmed cell death	0.004487	Inherited
Protein kinase-like (PK-like)	0.03174	Inherited
Caspase-like	0.04933	Inherited
Intermediate filament protein, coiled coil region	0.05416	Inherited
DNA-glycosylase	0.1504	Inherited
Serine protease inhibitors	0.1504	Inherited
Prefoldin	0.4842	Inherited
Ubiquitin-like	0.4922	Inherited
Thioredoxin-like	0.5343	Inherited
Ran binding protein zinc finger-like	0.7733	Inherited
HMG-box	0.8297	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)
54236,57889 54236 - Ubiquitin-like 57889 - Cysteine-rich domain	0	Direct
57196,69687 57196 - EGF/Laminin 69687 - Integrin beta tail domain	0	Direct
57362,57362 57362 - BPTI-like 57362 - BPTI-like	0	Direct
55753,55753 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins	0	Direct
57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0	Direct
57184,57603 57184 - Growth factor receptor domain 57603 - FnI-like domain	0	Direct
56672,100879 56672 - DNA/RNA polymerases 100879 - Lesion bypass DNA polymerase (Y-family), little finger domain	0	Direct
57603,82895 57603 - FnI-like domain 82895 - TSP-1 type 1 repeat	0	Direct
82153,82153 82153 - FAS1 domain 82153 - FAS1 domain	0	Direct
57196,90193 57196 - EGF/Laminin 90193 - Notch domain	0	Direct
90193,90193 90193 - Notch domain 90193 - Notch domain	0	Direct
53300,69179 53300 - vWA-like 69179 - Integrin domains	0	Direct
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like	0	Direct
49562,57889 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 57889 - Cysteine-rich domain	0	Direct
49417,47719 49417 - p53-like transcription factors 47719 - p53 tetramerization domain	0	Direct
53850,53850 53850 - Periplasmic binding protein-like II 53850 - Periplasmic binding protein-like II	0	Direct
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain	0	Direct
90188,53649 90188 - Somatomedin B domain 53649 - Alkaline phosphatase-like	0	Direct
57302,57302 57302 - Snake toxin-like 57302 - Snake toxin-like	0	Direct
57184,49265 57184 - Growth factor receptor domain 49265 - Fibronectin type III	0	Direct
47576,48065 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain)	0	Direct
47090,55486 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain	0.0003056	Direct
56112,47769 56112 - Protein kinase-like (PK-like) 47769 - SAM/Pointed domain	0.002666	Inherited
55486,50923 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain	0.004915	Inherited
49785,57184 49785 - Galactose-binding domain-like 57184 - Growth factor receptor domain	0.007422	Inherited
46579,64593 46579 - Prefoldin 64593 - Intermediate filament protein, coiled coil region	0.01389	Inherited
47986,52129 47986 - DEATH domain 52129 - Caspase-like	0.02019	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)
57196,57196,69687 57196 - EGF/Laminin 57196 - EGF/Laminin 69687 - Integrin beta tail domain	0	Direct
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain	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
90188,90188,53649 90188 - Somatomedin B domain 90188 - Somatomedin B domain 53649 - Alkaline phosphatase-like	0	Direct
52058,48726,48726 52058 - L domain-like 48726 - Immunoglobulin 48726 - Immunoglobulin	0	Direct
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like	0	Direct
47576,48065,50729 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0	Direct
57196,57196,90193 57196 - EGF/Laminin 57196 - EGF/Laminin 90193 - Notch domain	0	Direct
47986,47986,52129 47986 - DEATH domain 47986 - DEATH domain 52129 - Caspase-like	0	Direct
55753,55753,55753 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins	0	Direct
49785,57184,49265 49785 - Galactose-binding domain-like 57184 - Growth factor receptor domain 49265 - Fibronectin type III	0	Direct
49562,57889,57889 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 57889 - Cysteine-rich domain 57889 - Cysteine-rich domain	0	Direct
53067,53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain	0	Direct
47090,55486,50923 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain	0.001571	Inherited
55550,56112,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) 56112 - Protein kinase-like (PK-like)	0.1504	Inherited
50729,55550,56112 50729 - PH domain-like 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.1504	Inherited
57440,57440,57440 57440 - Kringle-like 57440 - Kringle-like 57440 - Kringle-like	0.5165	Inherited