Disease Ontology (DO): hematologic 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
TAFH domain-like	0	Direct
4-helical cytokines	0.00000007246	Direct
TNF receptor-like	0.0000001167	Direct
Inhibitor of apoptosis (IAP) repeat	0.0001254	Direct
A DNA-binding domain in eukaryotic transcription factors	0.000165	Direct
Leucine zipper domain	0.0002538	Direct
p53-like transcription factors	0.001442	Inherited
Bcl-2 inhibitors of programmed cell death	0.002943	Inherited
MHC antigen-recognition domain	0.003338	Inherited
Defensin-like	0.005877	Inherited
TNF-like	0.007035	Inherited
Frizzled cysteine-rich domain	0.009234	Inherited
Integrin domains	0.01292	Inherited
Transcription factor STAT-4 N-domain	0.01722	Inherited
STAT	0.01722	Inherited
Notch domain	0.02348	Inherited
Interleukin 8-like chemokines	0.02757	Inherited
PGBD-like	0.02919	Inherited
ABC transporter transmembrane region	0.03079	Inherited
Kringle-like	0.0459	Inherited
TIMP-like	0.06054	Inherited
SOCS box-like	0.07582	Inherited
HD-domain/PDEase-like	0.1187	Inherited
DPP6 N-terminal domain-like	0.1632	Inherited
Toll/Interleukin receptor TIR domain	0.181	Inherited
Hemopexin-like domain	0.181	Inherited
Cystine-knot cytokines	0.2149	Inherited
Arginase/deacetylase	0.4181	Inherited
SH2 domain	0.8738	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
C5 cytosine-specific DNA methylase, DCM	0	Direct
DNA ligase	0	Direct
TAFH domain-like	0	Direct
p53 tetramerization domain	0	Direct
BAFF receptor-like	0	Direct
Short-chain cytokines	0.000000008689	Direct
TNF receptor-like	0.000005252	Direct
Inhibitor of apoptosis (IAP) repeat	0.0000953	Direct
C2 set domains	0.0001274	Direct
A DNA-binding domain in eukaryotic transcription factors	0.0001274	Direct
Leucine zipper domain	0.0002352	Direct
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.0007943	Direct
Bcl-2 inhibitors of programmed cell death	0.002353	Inherited
MHC antigen-recognition domain	0.00292	Inherited
C1 set domains (antibody constant domain-like)	0.00292	Inherited
Defensin	0.004647	Inherited
L domain	0.005838	Inherited
Nucleoside diphosphate kinase, NDK	0.006024	Inherited
DEATH effector domain, DED	0.006024	Inherited
TNF-like	0.006097	Inherited
ABC transporter transmembrane region	0.007585	Inherited
Frizzled cysteine-rich domain	0.007722	Inherited
Integrin domains	0.01108	Inherited
STAT	0.0139	Inherited
Transcription factor STAT-4 N-domain	0.0139	Inherited
STAT DNA-binding domain	0.0139	Inherited
Fibronectin type II module	0.01722	Inherited
Notch domain	0.019	Inherited
MMP N-terminal domain	0.02527	Inherited
Interleukin 8-like chemokines	0.02564	Inherited
Interleukin-1 (IL-1)	0.02601	Inherited
DPP6 N-terminal domain-like	0.03983	Inherited
PDEase	0.06012	Inherited
Matrix metalloproteases, catalytic domain	0.06104	Inherited
SOCS box-like	0.06586	Inherited
ABC transporter ATPase domain-like	0.1263	Inherited
Toll/Interleukin receptor TIR domain	0.1382	Inherited
Hemopexin-like domain	0.1667	Inherited
Histone deacetylase, HDAC	0.2399	Inherited
SH2 domain	0.8423	Inherited
I set domains	0.853	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)
TAFH domain-like	0	Direct
p53 tetramerization domain	0	Direct
4-helical cytokines	0.00000003541	Direct
TNF receptor-like	0.0000000576	Direct
Inhibitor of apoptosis (IAP) repeat	0.00007431	Direct
A DNA-binding domain in eukaryotic transcription factors	0.00009852	Direct
Leucine zipper domain	0.0001531	Direct
p53-like transcription factors	0.0009203	Direct
Bcl-2 inhibitors of programmed cell death	0.001941	Inherited
MHC antigen-recognition domain	0.002223	Inherited
Defensin-like	0.004027	Inherited
TNF-like	0.004853	Inherited
Frizzled cysteine-rich domain	0.006408	Inherited
Integrin domains	0.009118	Inherited
STAT	0.01231	Inherited
Transcription factor STAT-4 N-domain	0.01231	Inherited
Notch domain	0.01717	Inherited
Nucleoside diphosphate kinase, NDK	0.01717	Inherited
Interleukin 8-like chemokines	0.02031	Inherited
PGBD-like	0.02161	Inherited
ABC transporter transmembrane region	0.02289	Inherited
Kringle-like	0.0348	Inherited
TIMP-like	0.04654	Inherited
SOCS box-like	0.05927	Inherited
HD-domain/PDEase-like	0.09496	Inherited
DPP6 N-terminal domain-like	0.1328	Inherited
Cytokine	0.1454	Inherited
Hemopexin-like domain	0.1483	Inherited
Toll/Interleukin receptor TIR domain	0.1483	Inherited
Cystine-knot cytokines	0.1784	Inherited
Arginase/deacetylase	0.3627	Inherited
SH2 domain	0.8018	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
57924,57924 57924 - Inhibitor of apoptosis (IAP) repeat 57924 - Inhibitor of apoptosis (IAP) repeat	0	Direct
57196,90193 57196 - EGF/Laminin 90193 - Notch domain	0	Direct
63501,50242 63501 - Frizzled cysteine-rich domain 50242 - TIMP-like	0	Direct
57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like	0.000001155	Direct
47986,47986 47986 - DEATH domain 47986 - DEATH domain	0.00007431	Direct
47454,57959 47454 - A DNA-binding domain in eukaryotic transcription factors 57959 - Leucine zipper domain	0.00009852	Direct
55550,55550 55550 - SH2 domain 55550 - SH2 domain	0.0003228	Direct
50729,56112 50729 - PH domain-like 56112 - Protein kinase-like (PK-like)	0.000389	Direct
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0.0008614	Direct
54452,48726 54452 - MHC antigen-recognition domain 48726 - Immunoglobulin	0.002407	Inherited
50729,55550 50729 - PH domain-like 55550 - SH2 domain	0.00518	Inherited
57184,52058 57184 - Growth factor receptor domain 52058 - L domain-like	0.00518	Inherited
52058,57184 52058 - L domain-like 57184 - Growth factor receptor domain	0.00518	Inherited
82199,57667 82199 - SET domain 57667 - beta-beta-alpha zinc fingers	0.005437	Inherited
57196,57424 57196 - EGF/Laminin 57424 - LDL receptor-like module	0.005437	Inherited
57440,57440 57440 - Kringle-like 57440 - Kringle-like	0.008434	Inherited
55550,158235 55550 - SH2 domain 158235 - SOCS box-like	0.01231	Inherited
49417,55550 49417 - p53-like transcription factors 55550 - SH2 domain	0.01231	Inherited
48092,47655 48092 - Transcription factor STAT-4 N-domain 47655 - STAT	0.01231	Inherited
47655,49417 47655 - STAT 49417 - p53-like transcription factors	0.01231	Inherited
47090,55486 47090 - PGBD-like 55486 - Metalloproteases ("zincins"), catalytic domain	0.02161	Inherited
90123,52540 90123 - ABC transporter transmembrane region 52540 - P-loop containing nucleoside triphosphate hydrolases	0.02289	Inherited
63825,57196 63825 - YWTD domain 57196 - EGF/Laminin	0.03599	Inherited
82171,53474 82171 - DPP6 N-terminal domain-like 53474 - alpha/beta-Hydrolases	0.03599	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)
50729,55550,56112 50729 - PH domain-like 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0	Direct
55550,56112,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) 56112 - Protein kinase-like (PK-like)	0	Direct
47986,47986,52129 47986 - DEATH domain 47986 - DEATH domain 52129 - Caspase-like	0	Direct
57196,57196,90193 57196 - EGF/Laminin 57196 - EGF/Laminin 90193 - Notch 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
57586,57586,57586 57586 - TNF receptor-like 57586 - TNF receptor-like 57586 - TNF receptor-like	0.000389	Direct
52058,57184,52058 52058 - L domain-like 57184 - Growth factor receptor domain 52058 - L domain-like	0.00518	Inherited
57196,57424,57424 57196 - EGF/Laminin 57424 - LDL receptor-like module 57424 - LDL receptor-like module	0.005437	Inherited
82199,57667,57667 82199 - SET domain 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.005437	Inherited
63825,57196,57424 63825 - YWTD domain 57196 - EGF/Laminin 57424 - LDL receptor-like module	0.005437	Inherited
48092,47655,49417 48092 - Transcription factor STAT-4 N-domain 47655 - STAT 49417 - p53-like transcription factors	0.01231	Inherited
47655,49417,55550 47655 - STAT 49417 - p53-like transcription factors 55550 - SH2 domain	0.01231	Inherited
57440,57440,57440 57440 - Kringle-like 57440 - Kringle-like 57440 - Kringle-like	0.03599	Inherited