Phenotypic Abnormality (PA): Abnormal digit morphology

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Phenotype Ontology
Like Gene Ontology (GO), phenotypy 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. Phenotype ontologies we have incorporated are as follows:

Disease Ontology (DO) Ontology (DO)
DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI thesaurus, SNOMED and OMIM.
Human Phenotype (HP) Ontology (HP)
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)
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)
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 (YP)
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)
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)
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)
ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
Xenopus Anatomy (XA) Ontology (XA)
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 (AP)
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 (EC)
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.
DrugBank ATC (DB) Ontology (DB)
In the Anatomical Therapeutic Chemical (ATC) classification system, drugs are classified in groups at five different levels according to the organ or system (1st level, anatomical main group) on which they act and their therapeutic (2nd level, therapeutic subgroup), pharmacological (3rd level, pharmacological subgroup) and chemical properties (4th level, chemical subgroup; 5th level, chemical substance). Only drugs in DrugBank are considered.
UniProtKB KeyWords (KW) Ontology (KW)
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).
UniProtKB UniPathway (UP) Ontology (UP)
UP is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as controlled vocabulary for pathway annotation in UniProtKB.

Structural Domain Phenotype Ontology and its Annotations
Structural Classification of Proteins (SCOP) classifies evolutionary-related domains into Superfamily level and Family level. Using the phenotype ontologies above, we have generated the domain-centric phenotype annotations, and further identified those phenotype terms which are the most informative to annotate SCOP domains. Promisingly, domain-centric phenotypic annotations can serve as an alternative starting point to explore genotype-phenotype relationships. We provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

Structural Domain Disease Ontology (DO) Ontology (SDDO) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DO.txt, and the corresponding ontology:SDDO.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Human Phenotype (HP) Ontology (SDHP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2HP.txt, and the corresponding ontology:SDHP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Mouse Phenotype (MP) Ontology (SDMP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2MP.txt, and the corresponding ontology:SDMP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Worm Phenotype (WP) Ontology (SDWP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2WP.txt, and the corresponding ontology:SDWP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Yeast Phenotype (YP) Ontology (SDYP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2YP.txt, and the corresponding ontology:SDYP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Fly Phenotype (FP) Ontology (SDFP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FP.txt, and the corresponding ontology:SDFP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Fly Anatomy (FA) Ontology (SDFA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FA.txt, and the corresponding ontology:SDFA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Zebrafish Anatomy (ZA) Ontology (SDZA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2ZA.txt, and the corresponding ontology:SDZA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Xenopus Anatomy (XA) Ontology (SDXA) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2XA.txt, and the corresponding ontology:SDXA.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Arabidopsis Plant Ontology (AP) Ontology (SDAP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2AP.txt, and the corresponding ontology:SDAP.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain Enzyme Commission (EC) Ontology (SDEC) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2EC.txt, and the corresponding ontology:SDEC.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain DrugBank ATC (DB) Ontology (SDDB) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DB.txt, and the corresponding ontology:SDDB.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain UniProtKB KeyWords (KW) Ontology (SDKW) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2KW.txt, and the corresponding ontology:SDKW.txt) and mysql tables (Domain2PO.sql.gz).
Structural Domain UniProtKB UniPathway (UP) Ontology (SDUP) and its Annotations:
For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2UP.txt, and the corresponding ontology:SDUP.txt) and mysql tables (Domain2PO.sql.gz).

Supra-domain Phenotype Ontology and its Annotations
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are interested in domain combinations. Also, we provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

Supra-domain Domain Disease Ontology (DO) Ontology (SPDO) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DO.txt, and the corresponding ontology:SPDO.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Human Phenotype (HP) Ontology (SPHO) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2HP.txt, and the corresponding ontology:SPHO.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Mouse Phenotype (MP) Ontology (SPMP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2MP.txt, and the corresponding ontology:SPMP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Worm Phenotype (WP) Ontology (SPWP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2WP.txt, and the corresponding ontology:SPWP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Yeast Phenotype (YP) Ontology (SPYP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2YP.txt, and the corresponding ontology:SPYP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Fly Phenotype (FP) Ontology (SPFP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FP.txt, and the corresponding ontology:SPFP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Fly Anatomy (FA) Ontology (SPFA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FA.txt, and the corresponding ontology:SPFA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Zebrafish Anatomy (ZA) Ontology (SPZA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2ZA.txt, and the corresponding ontology:SPZA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Xenopus Anatomy (XA) Ontology (SPXA) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2XA.txt, and the corresponding ontology:SPXA.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Arabidopsis Plant Ontology (AP) Ontology (SPAP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2AP.txt, and the corresponding ontology:SPAP.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain Enzyme Commission (EC) Ontology (SPEC) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2EC.txt, and the corresponding ontology:SPEC.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain DrugBank ATC (DB) Ontology (SPDB) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DB.txt, and the corresponding ontology:SPDB.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain UniProtKB KeyWords (KW) Ontology (SPKW) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2KW.txt, and the corresponding ontology:SPKW.txt) and mysql tables (SP2PO.sql.gz).
Supra-domain Domain UniProtKB UniPathway (UP) Ontology (SPUP) and its Annotations:
For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2UP.txt, and the corresponding ontology:SPUP.txt) and mysql tables (SP2PO.sql.gz).

Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]

Root: HP Hierarchy (human phenotype with 3 sub-ontologies PA, MI, ON)

Shortest distance to current term (+ for parents, - for children) HP term [HP ID] <#Children> (#SF|#FA) #Supra-domain
(Single|Duplex|Triple)

+ + + + 4: Phenotypic abnormality [HP:0000118] <25>

+ + + 3: Abnormality of limbs [HP:0040064] <8> (58|66) (63|33|25)

+ + + 3: Abnormality of skeletal morphology [HP:0011842] <17> (86|89) (90|52|33)

+ + + 3: Abnormality of the skeletal system [HP:0000924] <7> (88|98) (93|55|34)

+ + 2: Abnormality of limb bone [HP:0040068] <1> (29|32) (33|18|20)

+ + 2: Abnormal appendicular skeleton morphology [HP:0011844] <4> (35|43) (39|23|23)

+ 1: Abnormality of limb bone morphology [HP:0002813] <13> (29|32) (32|18|20)

0: Abnormal digit morphology [HP:0011297] <10> (16|21) (18|14|16)

- 1: Abnormality of toe [HP:0001780] <27> (6|7) (8|4|2)

- 1: Abnormality of finger [HP:0001167] <24> (12|16) (13|9|10)

- 1: Polydactyly [HP:0010442] <6> (2|2) (3|2|0)

- 1: Broad phalanx [HP:0006009] <3> (0|0) (0|0|0)

- 1: Short digit [HP:0011927] <3> (3|4) (4|4|4)

- 1: Syndactyly [HP:0001159] <3> (1|2) (1|0|0)

- 1: Clinodactyly [HP:0030084] <2> (0|3) (2|0|0)

- 1: Clubbing [HP:0001217] <2> (0|1) (0|0|1)

- 1: Macrodactyly [HP:0004099] <2> (0|0) (0|0|0)

- 1: Oligodactyly [HP:0012165] <2> (0|0) (0|0|0)

Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]

Superfamily

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SCOP term	FDR (all)	Annotation (direct or inherited)
TB module/8-cys domain	0	Direct
RuvA domain 2-like	0	Direct
Hect, E3 ligase catalytic domain	0.0007798	Direct
WD40 repeat-like	0.0263	Inherited
Restriction endonuclease-like	0.02959	Inherited
Insulin-like	0.02959	Inherited
ARID-like	0.03378	Inherited
Multidrug efflux transporter AcrB transmembrane domain	0.07448	Inherited
GroEL equatorial domain-like	0.07448	Inherited
HLH, helix-loop-helix DNA-binding domain	0.09947	Inherited
HMG-box	0.1779	Inherited
Cystine-knot cytokines	0.3461	Inherited
vWA-like	0.6673	Inherited
Immunoglobulin	0.6821	Inherited
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.707	Inherited
Class II aaRS and biotin synthetases	0.9231	Inherited

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Family

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SCOP term	FDR (all)	Annotation (direct or inherited)
Proteasome subunits	0	Direct
XPF/Rad1/Mus81 nuclease	0	Direct
Exostosin	0	Direct
TB module/8-cys domain	0	Direct
Hect, E3 ligase catalytic domain	0.0003809	Direct
Erythroid transcription factor GATA-1	0.0007066	Direct
VWC domain	0.00893	Inherited
Classic zinc finger, C2H2	0.01278	Inherited
ZZ domain	0.02007	Inherited
Insulin-like	0.02007	Inherited
ARID domain	0.02303	Inherited
HLH, helix-loop-helix DNA-binding domain	0.07265	Inherited
HMG-box	0.1394	Inherited
RecA protein-like (ATPase-domain)	0.1732	Inherited
I set domains	0.2943	Inherited
Tetratricopeptide repeat (TPR)	0.3224	Inherited
Transforming growth factor (TGF)-beta	0.3546	Inherited
Homeodomain	0.4284	Inherited
Integrin A (or I) domain	0.4287	Inherited
Actin/HSP70	0.4702	Inherited
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	0.8195	Inherited

Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term

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Supra-domain (including individual superfamily)

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Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
RuvA domain 2-like	0	Direct
TB module/8-cys domain	0	Direct
Hect, E3 ligase catalytic domain	0.0004058	Direct
WD40 repeat-like	0.01826	Inherited
Insulin-like	0.02075	Inherited
Restriction endonuclease-like	0.02075	Inherited
ARID-like	0.02396	Inherited
Multidrug efflux transporter AcrB transmembrane domain	0.05703	Inherited
GroEL equatorial domain-like	0.05703	Inherited
HLH, helix-loop-helix DNA-binding domain	0.07811	Inherited
HMG-box	0.1469	Inherited
Cystine-knot cytokines	0.3045	Inherited
Cysteine proteinases	0.3634	Inherited
vWA-like	0.6272	Inherited
TPR-like	0.6417	Inherited
Immunoglobulin	0.6426	Inherited
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	0.6681	Inherited
Class II aaRS and biotin synthetases	0.8955	Inherited

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Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
57581,57196 57581 - TB module/8-cys domain 57196 - EGF/Laminin	0	Direct
52980,47781 52980 - Restriction endonuclease-like 47781 - RuvA domain 2-like	0	Direct
57196,57581 57196 - EGF/Laminin 57581 - TB module/8-cys domain	0	Direct
57184,57581 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain	0	Direct
57581,57184 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain	0	Direct
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0.0005123	Direct
103575,48726 103575 - Plexin repeat 48726 - Immunoglobulin	0.02075	Inherited
57903,57903 57903 - FYVE/PHD zinc finger 57903 - FYVE/PHD zinc finger	0.02396	Inherited
53300,53300 53300 - vWA-like 53300 - vWA-like	0.05703	Inherited
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.1177	Inherited
48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin	0.2616	Inherited
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.37	Inherited
48452,48452 48452 - TPR-like 48452 - TPR-like	0.4501	Inherited
50729,50729 50729 - PH domain-like 50729 - PH domain-like	0.6681	Inherited

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Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
57196,57581,57196 57196 - EGF/Laminin 57581 - TB module/8-cys domain 57196 - EGF/Laminin	0	Direct
57184,57581,57196 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain 57196 - EGF/Laminin	0	Direct
57196,57196,57581 57196 - EGF/Laminin 57196 - EGF/Laminin 57581 - TB module/8-cys domain	0	Direct
57184,57184,57196 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57196 - EGF/Laminin	0	Direct
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 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
57581,57196,57581 57581 - TB module/8-cys domain 57196 - EGF/Laminin 57581 - TB module/8-cys domain	0	Direct
57184,57184,57581 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain	0	Direct
57581,57196,57196 57581 - TB module/8-cys domain 57196 - EGF/Laminin 57196 - EGF/Laminin	0	Direct
57184,57581,57184 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain	0	Direct
57196,57581,57184 57196 - EGF/Laminin 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain	0	Direct
57581,57184,57581 57581 - TB module/8-cys domain 57184 - Growth factor receptor domain 57581 - TB module/8-cys domain	0	Direct
101912,103575,48726 101912 - Sema domain 103575 - Plexin repeat 48726 - Immunoglobulin	0.02075	Inherited
52540,52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0.08569	Inherited
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin	0.1531	Inherited
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.4094	Inherited

Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term

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Phenotypic Abnormality (PA): Abnormal digit morphology

Superfamily

Family

Supra-domain (including individual superfamily)