Phenotypic Abnormality (PA): Abnormality of the respiratory system

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)
Notch domain	0	Direct
Tricorn protease domain 2	0	Direct
Plakin repeat	0	Direct
Saposin	0	Direct
Lipoxigenase	0	Direct
Actin depolymerizing proteins	0	Direct
p53-like transcription factors	0.0001419	Direct
SH2 domain	0.0001677	Direct
4-helical cytokines	0.01016	Inherited
DEATH domain	0.02235	Inherited
Growth factor receptor domain	0.02313	Inherited
TB module/8-cys domain	0.03546	Inherited
Calcium-dependent phosphotriesterase	0.07072	Inherited
RuvA domain 2-like	0.07072	Inherited
Neurotransmitter-gated ion-channel transmembrane pore	0.1274	Inherited
Nicotinic receptor ligand binding domain-like	0.1274	Inherited
MHC antigen-recognition domain	0.1584	Inherited
GLA-domain	0.1673	Inherited
Cystine-knot cytokines	0.2068	Inherited
EGF/Laminin	0.2543	Inherited
TNF receptor-like	0.2877	Inherited
Ubiquitin-like	0.3727	Inherited
Snake toxin-like	0.3915	Inherited
Tropomyosin	0.4753	Inherited
RNA-binding domain, RBD	0.4867	Inherited
Intermediate filament protein, coiled coil region	0.6372	Inherited
ABC transporter transmembrane region	0.7818	Inherited
WD40 repeat-like	0.8292	Inherited
Voltage-gated potassium channels	0.8658	Inherited
vWA-like	0.9295	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)
Filamin repeat (rod domain)	0	Direct
Animal lipoxigenases	0	Direct
Serum paraoxonase/arylesterase 1, PON1	0	Direct
Rel/Dorsal transcription factors, DNA-binding domain	0	Direct
beta-glycanases	0	Direct
Notch domain	0	Direct
Plakin repeat	0	Direct
SH2 domain	0.00008414	Direct
Growth factor receptor domain	0.0001971	Direct
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.0116	Inherited
Transcription factor STAT-4 N-domain	0.0116	Inherited
Ras-binding domain, RBD	0.0116	Inherited
STAT DNA-binding domain	0.0116	Inherited
STAT	0.0116	Inherited
TB module/8-cys domain	0.02549	Inherited
DEATH domain, DD	0.02912	Inherited
C1 set domains (antibody constant domain-like)	0.02912	Inherited
VWC domain	0.03837	Inherited
ZZ domain	0.0547	Inherited
Neurotransmitter-gated ion-channel transmembrane pore	0.1023	Inherited
Nicotinic receptor ligand binding domain-like	0.1023	Inherited
Tetratricopeptide repeat (TPR)	0.1183	Inherited
Laminin-type module	0.1235	Inherited
MHC antigen-recognition domain	0.1299	Inherited
GLA-domain	0.1384	Inherited
MIR domain	0.1384	Inherited
Arylsulfatase	0.2006	Inherited
RecA protein-like (ATPase-domain)	0.2006	Inherited
Eukaryotic proteases	0.3116	Inherited
Canonical RBD	0.3116	Inherited
Tropomyosin	0.4339	Inherited
ABC transporter ATPase domain-like	0.5788	Inherited
Intermediate filament protein, coiled coil region	0.5982	Inherited
Integrin A (or I) domain	0.7505	Inherited
ABC transporter transmembrane region	0.7552	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)
Notch domain	0	Direct
Plakin repeat	0	Direct
Actin depolymerizing proteins	0	Direct
Tricorn protease domain 2	0	Direct
Lipoxigenase	0	Direct
Saposin	0	Direct
p53-like transcription factors	0.00006643	Direct
SH2 domain	0.00007915	Direct
4-helical cytokines	0.006545	Inherited
Transcription factor STAT-4 N-domain	0.0115	Inherited
STAT	0.0115	Inherited
DEATH domain	0.01537	Inherited
Growth factor receptor domain	0.01594	Inherited
RCC1/BLIP-II	0.01936	Inherited
TB module/8-cys domain	0.0253	Inherited
Adenine nucleotide alpha hydrolases-like	0.03787	Inherited
RuvA domain 2-like	0.05391	Inherited
Calcium-dependent phosphotriesterase	0.05391	Inherited
Immunoglobulin	0.08329	Inherited
Nicotinic receptor ligand binding domain-like	0.1023	Inherited
Neurotransmitter-gated ion-channel transmembrane pore	0.1023	Inherited
MHC antigen-recognition domain	0.1296	Inherited
GLA-domain	0.1375	Inherited
MIR domain	0.1375	Inherited
Cystine-knot cytokines	0.1736	Inherited
Trypsin-like serine proteases	0.2155	Inherited
EGF/Laminin	0.2171	Inherited
TNF receptor-like	0.2485	Inherited
Ubiquitin-like	0.3298	Inherited
Snake toxin-like	0.3482	Inherited
Tropomyosin	0.4314	Inherited
RNA-binding domain, RBD	0.4427	Inherited
Intermediate filament protein, coiled coil region	0.5961	Inherited
ABC transporter transmembrane region	0.7456	Inherited
WD40 repeat-like	0.7958	Inherited
Voltage-gated potassium channels	0.8343	Inherited
vWA-like	0.9024	Inherited
Glucocorticoid receptor-like (DNA-binding domain)	0.9605	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)
50729,55550 50729 - PH domain-like 55550 - SH2 domain	0	Direct
57581,57184 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain	0	Direct
54928,90209 54928 - RNA-binding domain, RBD 90209 - Ran binding protein zinc finger-like	0	Direct
49265,48726 49265 - Fibronectin type III 48726 - Immunoglobulin	0	Direct
49723,48484 49723 - Lipase/lipooxygenase domain (PLAT/LH2 domain) 48484 - Lipoxigenase	0	Direct
57184,57581 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain	0	Direct
49417,81296 49417 - p53-like transcription factors 81296 - E set domains	0	Direct
55550,55550 55550 - SH2 domain 55550 - SH2 domain	0	Direct
75399,75399 75399 - Plakin repeat 75399 - Plakin repeat	0	Direct
57196,90193 57196 - EGF/Laminin 90193 - Notch domain	0	Direct
56112,56112 56112 - Protein kinase-like (PK-like) 56112 - Protein kinase-like (PK-like)	0	Direct
49417,55550 49417 - p53-like transcription factors 55550 - SH2 domain	0.0115	Inherited
47655,49417 47655 - STAT 49417 - p53-like transcription factors	0.0115	Inherited
48092,47655 48092 - Transcription factor STAT-4 N-domain 47655 - STAT	0.0115	Inherited
57196,57581 57196 - EGF/Laminin 57581 - TB module/8-cys domain	0.0253	Inherited
57581,57196 57581 - TB module/8-cys domain 57196 - EGF/Laminin	0.0253	Inherited
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.02738	Inherited
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.07879	Inherited
63712,90112 63712 - Nicotinic receptor ligand binding domain-like 90112 - Neurotransmitter-gated ion-channel transmembrane pore	0.1023	Inherited
54452,48726 54452 - MHC antigen-recognition domain 48726 - Immunoglobulin	0.1296	Inherited
53300,53300 53300 - vWA-like 53300 - vWA-like	0.1338	Inherited
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.2156	Inherited
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD	0.299	Inherited
90123,52540 90123 - ABC transporter transmembrane region 52540 - P-loop containing nucleoside triphosphate hydrolases	0.7456	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)
48726,49265,48726 48726 - Immunoglobulin 49265 - Fibronectin type III 48726 - Immunoglobulin	0	Direct
57184,57581,57196 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain 57196 - EGF/Laminin	0	Direct
55550,56112,56112 55550 - SH2 domain 56112 - Protein kinase-like (PK-like) 56112 - Protein kinase-like (PK-like)	0	Direct
57581,57184,57581 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain	0	Direct
57184,52058,57184 57184 - Growth factor receptor domain 52058 - L domain-like 57184 - Growth factor receptor domain	0	Direct
57184,57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0	Direct
57184,57581,57184 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain	0	Direct
57184,57184,57581 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain	0	Direct
57184,57196,57184 57184 - Growth factor receptor domain 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0	Direct
50729,55550,56112 50729 - PH domain-like 55550 - SH2 domain 56112 - Protein kinase-like (PK-like)	0	Direct
57196,57196,90193 57196 - EGF/Laminin 57196 - EGF/Laminin 90193 - Notch domain	0	Direct
52540,52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0.002129	Inherited
48092,47655,49417 48092 - Transcription factor STAT-4 N-domain 47655 - STAT 49417 - p53-like transcription factors	0.0115	Inherited
47655,49417,55550 47655 - STAT 49417 - p53-like transcription factors 55550 - SH2 domain	0.0115	Inherited
57581,57196,57581 57581 - TB module/8-cys domain 57196 - EGF/Laminin 57581 - TB module/8-cys domain	0.0253	Inherited
57581,57196,57196 57581 - TB module/8-cys domain 57196 - EGF/Laminin 57196 - EGF/Laminin	0.0253	Inherited
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.03787	Inherited
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.04806	Inherited
57184,57184,57196 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57196 - EGF/Laminin	0.05391	Inherited
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin	0.2932	Inherited
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin	0.3382	Inherited