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+ + + + + + + + + + + + + + +This file provides the disease to gene mappings that are used to create the phenotype.hpoa file.
+ncbi_gene_id | +gene_symbol | +association_type | +disease_id | +source | +
---|---|---|---|---|
NCBIGene:64170 | +CARD9 | +MENDELIAN | +OMIM:212050 | +ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/mim2gene_medgen | +
NCBIGene:51256 | +TBC1D7 | +MENDELIAN | +OMIM:248000 | +ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/mim2gene_medgen | +
NCBIGene:28981 | +IFT81 | +MENDELIAN | +OMIM:617895 | +ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/mim2gene_medgen | +
NCBIGene:8216 | +LZTR1 | +MENDELIAN | +OMIM:616564 | +ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/mim2gene_medgen | +
The association types are:
+In the genes_to_phenotypes.txt file, we list for each gene the most specific HPO-classes (and not all the ancestors). The following table shows an excerpt from the file. The table provides the NCBI Gene identifier, the gene symbol, the HPO identifier and term name. If available, the frequency is shown. For instance, mutation in the AARS1 gene cause Leukoencephalopathy, hereditary diffuse, with spheroids 2. The frequency of the HPO term Sensory ataxia was annotated to be 1 in 2 because of information in Sundal C, et al., PMID:31775912 (See entry in table below). The HPO resource offers annotations made by the HPO team (using disease identifiers from OMIM) as well as annotations provided by the Orphanet team (using ORPHA disease identifiers). In this case, gene to phenotype annotations are shown separately.
+ncbi_gene_id | +gene_symbol | +hpo_id | +hpo_name | +frequency | +disease_id | +
---|---|---|---|---|---|
10 | +NAT2 | +HP:0000007 | +Autosomal recessive inheritance | +- | +OMIM:243400 | +
10 | +NAT2 | +HP:0001939 | +Abnormality of metabolism/homeostasis | +- | +OMIM:243400 | +
16 | +AARS1 | +HP:0002460 | +Distal muscle weakness | +15/15 | +OMIM:613287 | +
16 | +AARS1 | +HP:0002451 | +Limb dystonia | +3/3 | +OMIM:616339 | +
16 | +AARS1 | +HP:0010871 | +Sensory ataxia | +1/2 | +OMIM:619661 | +
16 | +AARS1 | +HP:0009886 | +Trichorrhexis nodosa | +1/2 | +OMIM:619691 | +
16 | +AARS1 | +HP:0002421 | +Poor head control | +HP:0040283 | +ORPHA:442835 | +
16 | +AARS1 | +HP:0001298 | +Encephalopathy | +HP:0040281 | +ORPHA:442835 | +
16 | +AARS1 | +HP:0001290 | +Generalized hypotonia | +HP:0040282 | +ORPHA:442835 | +
16 | +AARS1 | +HP:0001273 | +Abnormal corpus callosum morphology | +HP:0040283 | +ORPHA:442835 | +
16 | +AARS1 | +HP:0001268 | +Mental deterioration | +HP:0040283 | +ORPHA:442835 | +
16 | +AARS1 | +HP:0001268 | +Mental deterioration | +2/2 | +OMIM:619661 | +
In addition to the ontology itself, we provide HPO annotations (HPOAs) of diseases. For instance, the disease Marfan syndrome is characterized by—and therefore annotated to—over 50 phenotypic abnormalities including Aortic aneurysm (each abnormality is represented by an HPO term). The annotations can have modifiers that describe the age of onset and the frequencies of features. For instance, the phenotypic abnormality Chiari malformation is rare in Loeys-Dietz syndrome 1 (4/30 according to a published study referenced in our data), but affects nearly 100% of patients diagnosed with most of the 446284 other diseases annotated to this term. The annotations include phenotypic abnormalities that are never present in a disease, and their absence can be leveraged in the differential diagnosis of diseases with overlapping clinical features. For instance, Ectopia lentis is not a characteristic of Loeys-Dietz syndrome 1 , whereas it is frequently observed in subjects with Marfan syndrome . The age of onset, frequency, and absence of the phenotypic features can be used by algorithms to weight findings in the context of clinical differential diagnosis.
+The annotation data of the HPO project is made available in the phenotype.hpoa file. We additionally provide three other files with summary-level information derived from the annotations.
+ + + + + + + + + + + + + + +The HPO project provides a comprehensive set of computable definitions of rare diseases in the form of annotations which describe the clinical features (HPO terms) that characterize each disease. Each annotated feature can have metadata including its typical age of onset and the frequency. Ror instance, the HPO lists the frequency of Protrusio acetabuli in persons with Marfan syndrome as 113/146 based on a published clinical study (PMID:26339165).
+Field | +Item | +Required | +Example | +
---|---|---|---|
1 | +database_id | +Yes | +MIM:154700, ORPHA:558 or MONDO:0007947 | +
2 | +disease_name | +Yes | +Achondrogenesis, type IB | +
3 | +qualifier | +No | +NOT or empty | +
4 | +hpo_id | +Yes | +HP:0002487 | +
5 | +reference | +Yes | +OMIM:154700 or PMID:15517394 | +
6 | +Evidence | +Yes | +IEA or PCS | +
7 | +Onset | +No | +HP:0003577 | +
8 | +Frequency | +No | +HP:0003577 or 12/45 or 22% | +
9 | +Sex | +No | +MALE or FEMALE | +
10 | +Modifier | +No | +HP:0025257 | +
11 | +Aspect | +Yes | +‘P’ or ‘C’ or ‘I’, 'H', or ‘M’ | +
12 | +BiocurationBy | +Yes | +HPO:skoehler[YYYY-MM-DD] | +
The file contains 12 tab-separated fields, some of which can be left empty. The ‘Modifier’ and ‘BiocurationBy’ fields can contain multiple items separated by semicolons. For instance, to indicate that a disease is characterized by a skin rash (HP:0000988) that is Recurrent (HP:0031796) and Triggered by cold (HP:0025206) one would annotate HP:0031796;HP:0025206 in the Modifier column. Many annotations go through multiple stages of biocuration. In this case, the individual biocuration events are also added as a semicolon-separated list.
+aspect: This field denotes what part of the HPO hierarchy an annotation comes from. For use in semantic similarity analysis, some approaches use only terms that descend from Phenotypic abnormality and filter other annotations out.
+ +biocuration: e.g., HPO:skoehler[YYYY-MM-DD]
+The phenotype_to_genes.txt file displays the HPO identifier and term name, the NCBI Gene identifier, the gene symbol, and the disease identifier. This file shows each HPO term that has at least one gene associated with it. In contrast to the genes_to_phenotypes.txt file, this file includes the ancestor classes of each associated phenotype. For example given that:
+then genes_to_phenotypes.txt would have:
+then phenotype_to_genes.txt contains:
+Here is a sample of the file format.
+hpo_id | +hpo_name | +ncbi_gene_id | +gene_symbol | +disease_id | +
---|---|---|---|---|
HP:0003300 | +Ovoid vertebral bodies | +1280 | +COL2A1 | +OMIM:184255 | +
HP:0003300 | +Ovoid vertebral bodies | +1280 | +COL2A1 | +OMIM:271700 | +
HP:0003300 | +Ovoid vertebral bodies | +1280 | +COL2A1 | +OMIM:151210 | +
HP:0003300 | +Ovoid vertebral bodies | +1280 | +COL2A1 | +ORPHA: | +
HP:0003300 | +Ovoid vertebral bodies | +1280 | +COL2A1 | +OMIM:183900 | +
HP:0003300 | +Ovoid vertebral bodies | +1280 | +COL2A1 | +ORPHA:1856 | +
HP:0003300 | +Ovoid vertebral bodies | +2335 | +FN1 | +OMIM:184255 | +
HP:0003300 | +Ovoid vertebral bodies | +2335 | +FN1 | +ORPHA:93315 | +
HP:0003300 | +Ovoid vertebral bodies | +126792 | +B3GALT6 | +ORPHA:536467 | +
HP:0003300 | +Ovoid vertebral bodies | +126792 | +B3GALT6 | +OMIM:271640 | +
HP:0003300 | +Ovoid vertebral bodies | +4882 | +NPR2 | +OMIM:602875 | +
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+ * escape-html
+ * Copyright(c) 2012-2013 TJ Holowaychuk
+ * Copyright(c) 2015 Andreas Lubbe
+ * Copyright(c) 2015 Tiancheng "Timothy" Gu
+ * MIT Licensed
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