Fly Anatomy (FA): adult head

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

Jump to [ Top · Hierarchy ]

Superfamily

(show details)

SCOP term	FDR (all)	Annotation (direct or inherited)
Thiamin diphosphate-binding fold (THDP-binding)	0	Direct
Frizzled cysteine-rich domain	0	Direct
SAP domain	0	Direct
Second domain of FERM	0.00007703	Direct
Caspase-like	0.004052	Inherited
SH2 domain	0.03169	Inherited
Cadherin-like	0.03837	Inherited
(Phosphotyrosine protein) phosphatases II	0.06808	Inherited
lambda repressor-like DNA-binding domains	0.1198	Inherited
dsRNA-binding domain-like	0.1574	Inherited
Immunoglobulin	0.2265	Inherited
Fibronectin type III	0.2927	Inherited
EGF/Laminin	0.3028	Inherited
Growth factor receptor domain	0.4258	Inherited
HAD-like	0.672	Inherited
Homeodomain-like	0.7314	Inherited
TPR-like	0.9283	Inherited
HLH, helix-loop-helix DNA-binding domain	1	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Family

Jump to [ Top · Hierarchy ]

Family

(show details)

SCOP term	FDR (all)	Annotation (direct or inherited)
p120GAP domain-like	0	Direct
Frizzled cysteine-rich domain	0	Direct
Group II chaperonin (CCT, TRIC), intermediate domain	0	Direct
VHS domain	0	Direct
Diacylglycerol kinase-like	0	Direct
SAP domain	0	Direct
Integrin domains	0	Direct
Group II chaperonin (CCT, TRIC), ATPase domain	0	Direct
Group II chaperonin (CCT, TRIC), apical domain	0	Direct
Second domain of FERM	0.0000823	Direct
Third domain of FERM	0.0005986	Direct
Laminin G-like module	0.00145	Inherited
SH2 domain	0.03299	Inherited
Protein kinases, catalytic subunit	0.06083	Inherited
Cadherin	0.06894	Inherited
I set domains	0.1034	Inherited
POU-specific domain	0.1618	Inherited
Extracellular domain of cell surface receptors	0.2324	Inherited
Fibronectin type III	0.3148	Inherited
EGF-type module	0.3532	Inherited
Growth factor receptor domain	0.3634	Inherited
BTB/POZ domain	0.6219	Inherited
Homeodomain	0.8872	Inherited
HLH, helix-loop-helix DNA-binding domain	1	Inherited

LINKTO: Domain2BO Download and Domain2BO Algorithm

Supra-domain (Single|Duplex|Triple)

Jump to [ Top · Hierarchy ]

Supra-domain (Single)

(show details)

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
SAP domain	0	Direct
Thiamin diphosphate-binding fold (THDP-binding)	0	Direct
Frizzled cysteine-rich domain	0	Direct
Second domain of FERM	0.00005645	Direct
Caspase-like	0.002922	Inherited
SH2 domain	0.0248	Inherited
Cadherin-like	0.03019	Inherited
Protein kinase-like (PK-like)	0.04345	Inherited
Plexin repeat	0.05395	Inherited
(Phosphotyrosine protein) phosphatases II	0.05543	Inherited
lambda repressor-like DNA-binding domains	0.1011	Inherited
dsRNA-binding domain-like	0.1348	Inherited
Snake toxin-like	0.149	Inherited
Immunoglobulin	0.1988	Inherited
Fibronectin type III	0.2619	Inherited
EGF/Laminin	0.2722	Inherited
Growth factor receptor domain	0.3933	Inherited
HAD-like	0.6453	Inherited
Homeodomain-like	0.7084	Inherited
TPR-like	0.9185	Inherited
HLH, helix-loop-helix DNA-binding domain	1	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

Jump to [ Top · Hierarchy ]

Supra-domain (Duplex) in N- to C-terminal order

(show details)

Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
55550,50044 55550 - SH2 domain 50044 - SH3-domain	0	Direct
50044,55550 50044 - SH3-domain 55550 - SH2 domain	0	Direct
47031,50729 47031 - Second domain of FERM 50729 - PH domain-like	0.0004303	Direct
49899,49899 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0.0004303	Direct
54236,47031 54236 - Ubiquitin-like 47031 - Second domain of FERM	0.0004303	Direct
49313,49313 49313 - Cadherin-like 49313 - Cadherin-like	0.05788	Inherited
48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin	0.08604	Inherited
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like	0.1011	Inherited
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat	0.1011	Inherited
51045,51045 51045 - WW domain 51045 - WW domain	0.1011	Inherited
48726,49265 48726 - Immunoglobulin 49265 - Fibronectin type III	0.2015	Inherited
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.2184	Inherited
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.3178	Inherited
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III	0.4445	Inherited

LINKTO: Supra-domain2BO Download and Supra-domain2BO Algorithm

Jump to [ Top · Hierarchy ]

Supra-domain (Triple) in N- to C-terminal order

(show details)

Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
49899,49899,49899 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0	Direct
57196,49899,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0	Direct
54236,47031,50729 54236 - Ubiquitin-like 47031 - Second domain of FERM 50729 - PH domain-like	0.002922	Inherited
49313,49313,49313 49313 - Cadherin-like 49313 - Cadherin-like 49313 - Cadherin-like	0.05788	Inherited
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin	0.09806	Inherited
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin	0.1036	Inherited
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III	0.2552	Inherited