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)
Insulin-like	0	Direct
Purine and uridine phosphorylases	0	Direct
Integrin beta tail domain	0	Direct
Nuclear receptor coactivator interlocking domain	0	Direct
FAS1 domain	0	Direct
Di-copper centre-containing domain	0	Direct
HSP90 C-terminal domain	0	Direct
Synuclein	0	Direct
p53 tetramerization domain	0	Direct
Lesion bypass DNA polymerase (Y-family), little finger domain	0	Direct
PGBD-like	0.0005025	Direct
Metalloproteases ("zincins"), catalytic domain	0.0005542	Direct
Hemopexin-like domain	0.001836	Inherited
Growth factor receptor domain	0.004488	Inherited
Bcl-2 inhibitors of programmed cell death	0.006555	Inherited
Protein kinase-like (PK-like)	0.03863	Inherited
Caspase-like	0.0642	Inherited
Intermediate filament protein, coiled coil region	0.07014	Inherited
Prefoldin	0.5478	Inherited
Ubiquitin-like	0.5575	Inherited
Thioredoxin-like	0.602	Inherited
Ran binding protein zinc finger-like	0.846	Inherited
HMG-box	0.9011	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)
Hsp90 middle domain	0	Direct
Neurotrophin	0	Direct
HSP90 C-terminal domain	0	Direct
Purine and uridine phosphorylases	0	Direct
Nuclear receptor coactivator interlocking domain	0	Direct
Insulin-like	0	Direct
PAS domain of steroid receptor coactivator 1A, NCo-A1	0	Direct
Integrin beta tail domain	0	Direct
p53 tetramerization domain	0	Direct
Integrin beta EGF-like domains	0	Direct
Lesion bypass DNA polymerase (Y-family), catalytic domain	0	Direct
p53 DNA-binding domain-like	0	Direct
Tissue inhibitor of metalloproteinases, TIMP	0	Direct
Heat shock protein 90, HSP90, N-terminal domain	0	Direct
L domain	0	Direct
Gelsolin-like	0	Direct
DEATH effector domain, DED	0	Direct
Retinoblastoma tumor suppressor domains	0	Direct
Synuclein	0	Direct
FAS1 domain	0	Direct
Transferrin	0	Direct
Uteroglobin-like	0	Direct
S100 proteins	0.00005568	Direct
MMP N-terminal domain	0.0003818	Direct
Growth factor receptor domain	0.0004265	Direct
Matrix metalloproteases, catalytic domain	0.0008867	Direct
Hemopexin-like domain	0.001426	Inherited
Ephrin receptor ligand binding domain	0.003078	Inherited
Bcl-2 inhibitors of programmed cell death	0.005087	Inherited
Platelet-derived growth factor-like	0.0222	Inherited
Caspase catalytic domain	0.03281	Inherited
Hexokinase	0.04591	Inherited
Intermediate filament protein, coiled coil region	0.06637	Inherited
Protein kinases, catalytic subunit	0.07156	Inherited
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.1147	Inherited
Protein kinase cysteine-rich domain (cys2, phorbol-binding domain)	0.1163	Inherited
C5 cytosine-specific DNA methylase, DCM	0.1597	Inherited
Ras-binding domain, RBD	0.2436	Inherited
Ran binding protein zinc finger-like	0.8248	Inherited
HMG-box	0.8865	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)
Insulin-like	0	Direct
Integrin beta tail 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
Di-copper centre-containing domain	0	Direct
FAS1 domain	0	Direct
Synuclein	0	Direct
Purine and uridine phosphorylases	0	Direct
Nuclear receptor coactivator interlocking domain	0	Direct
PGBD-like	0.0003073	Direct
Metalloproteases ("zincins"), catalytic domain	0.0003401	Direct
Hemopexin-like domain	0.001185	Inherited
Growth factor receptor domain	0.003032	Inherited
Bcl-2 inhibitors of programmed cell death	0.004499	Inherited
Protein kinase-like (PK-like)	0.02893	Inherited
Caspase-like	0.04952	Inherited
Intermediate filament protein, coiled coil region	0.05443	Inherited
DNA-glycosylase	0.1505	Inherited
Serine protease inhibitors	0.1505	Inherited
Prefoldin	0.4848	Inherited
Ubiquitin-like	0.4937	Inherited
Thioredoxin-like	0.5354	Inherited
Ran binding protein zinc finger-like	0.7736	Inherited
HMG-box	0.8299	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
57184,57603 57184 - Growth factor receptor domain 57603 - FnI-like domain	0	Direct
57603,82895 57603 - FnI-like domain 82895 - TSP-1 type 1 repeat	0	Direct
57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0	Direct
49562,57889 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 57889 - Cysteine-rich domain	0	Direct
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain	0	Direct
82153,82153 82153 - FAS1 domain 82153 - FAS1 domain	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
53300,69179 53300 - vWA-like 69179 - Integrin domains	0	Direct
57196,90193 57196 - EGF/Laminin 90193 - Notch domain	0	Direct
57362,57362 57362 - BPTI-like 57362 - BPTI-like	0	Direct
90188,53649 90188 - Somatomedin B domain 53649 - Alkaline phosphatase-like	0	Direct
54236,57889 54236 - Ubiquitin-like 57889 - Cysteine-rich domain	0	Direct
47576,48065 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain)	0	Direct
55753,55753 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins	0	Direct
56672,100879 56672 - DNA/RNA polymerases 100879 - Lesion bypass DNA polymerase (Y-family), little finger domain	0	Direct
57196,69687 57196 - EGF/Laminin 69687 - Integrin beta tail domain	0	Direct
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like	0	Direct
90193,90193 90193 - Notch domain 90193 - Notch domain	0	Direct
53850,53850 53850 - Periplasmic binding protein-like II 53850 - Periplasmic binding protein-like II	0	Direct
47090,55486 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain	0.0003073	Direct
56112,47769 56112 - Protein kinase-like (PK-like) 47769 - SAM/Pointed domain	0.002675	Inherited
55486,50923 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain	0.004928	Inherited
49785,57184 49785 - Galactose-binding domain-like 57184 - Growth factor receptor domain	0.007448	Inherited
46579,64593 46579 - Prefoldin 64593 - Intermediate filament protein, coiled coil region	0.01391	Inherited
47986,52129 47986 - DEATH domain 52129 - Caspase-like	0.02024	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
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like	0	Direct
53067,53067,53067 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain	0	Direct
57196,57196,90193 57196 - EGF/Laminin 57196 - EGF/Laminin 90193 - Notch domain	0	Direct
55753,55753,55753 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins	0	Direct
49562,57889,57889 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 57889 - Cysteine-rich domain 57889 - Cysteine-rich domain	0	Direct
49785,57184,49265 49785 - Galactose-binding domain-like 57184 - Growth factor receptor domain 49265 - Fibronectin type III	0	Direct
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain	0	Direct
47986,47986,52129 47986 - DEATH domain 47986 - DEATH domain 52129 - Caspase-like	0	Direct
47576,48065,50729 47576 - Calponin-homology domain, CH-domain 48065 - DBL homology domain (DH-domain) 50729 - PH domain-like	0	Direct
90188,90188,53649 90188 - Somatomedin B domain 90188 - Somatomedin B domain 53649 - Alkaline phosphatase-like	0	Direct
57196,57196,69687 57196 - EGF/Laminin 57196 - EGF/Laminin 69687 - Integrin beta tail 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
47090,55486,50923 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain 50923 - Hemopexin-like domain	0.001578	Inherited
55550,56112,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) 56112 - Protein kinase-like (PK-like)	0.1505	Inherited
50729,55550,56112 50729 - PH domain-like 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0.1505	Inherited
57440,57440,57440 57440 - Kringle-like 57440 - Kringle-like 57440 - Kringle-like	0.5169	Inherited