| Title: | biodbUniprot, a library for connecting to the Uniprot Database |
|---|---|
| Description: | The biodbUniprot library is an extension of the biodb framework package. It provides access to the UniProt database. It allows to retrieve entries by their accession number, and run web service queries for searching for entries. |
| Authors: | Pierrick Roger [aut, cre] |
| Maintainer: | Pierrick Roger <[email protected]> |
| License: | AGPL-3 |
| Version: | 1.13.0 |
| Built: | 2024-10-30 04:23:08 UTC |
| Source: | https://github.com/bioc/biodbUniprot |
The connector class to Uniprot database.
The connector class to Uniprot database.
This is a concrete connector class. It must never be instantiated directly, but instead be instantiated through the factory BiodbFactory. Only specific methods are described here. See super classes for the description of inherited methods.
biodb::BiodbConnBase -> biodb::BiodbConn -> UniprotConn
biodb::BiodbConnBase$getBaseUrl()biodb::BiodbConnBase$getConnClass()biodb::BiodbConnBase$getConnClassName()biodb::BiodbConnBase$getDbClass()biodb::BiodbConnBase$getEntryClass()biodb::BiodbConnBase$getEntryClassName()biodb::BiodbConnBase$getEntryContentType()biodb::BiodbConnBase$getEntryFileExt()biodb::BiodbConnBase$getEntryIdField()biodb::BiodbConnBase$getName()biodb::BiodbConnBase$getPropSlots()biodb::BiodbConnBase$getPropValSlot()biodb::BiodbConnBase$getPropertyValue()biodb::BiodbConnBase$getSchedulerNParam()biodb::BiodbConnBase$getSchedulerTParam()biodb::BiodbConnBase$getToken()biodb::BiodbConnBase$getUrl()biodb::BiodbConnBase$getUrls()biodb::BiodbConnBase$getWsUrl()biodb::BiodbConnBase$getXmlNs()biodb::BiodbConnBase$hasProp()biodb::BiodbConnBase$hasPropSlot()biodb::BiodbConnBase$isSlotProp()biodb::BiodbConnBase$propExists()biodb::BiodbConnBase$setBaseUrl()biodb::BiodbConnBase$setPropValSlot()biodb::BiodbConnBase$setPropertyValue()biodb::BiodbConnBase$setSchedulerNParam()biodb::BiodbConnBase$setSchedulerTParam()biodb::BiodbConnBase$setToken()biodb::BiodbConnBase$setUrl()biodb::BiodbConnBase$setWsUrl()biodb::BiodbConnBase$updatePropertiesDefinition()biodb::BiodbConn$addNewEntry()biodb::BiodbConn$allowEditing()biodb::BiodbConn$allowWriting()biodb::BiodbConn$annotateMzValues()biodb::BiodbConn$checkDb()biodb::BiodbConn$collapseResultsDataFrame()biodb::BiodbConn$correctIds()biodb::BiodbConn$deleteAllCacheEntries()biodb::BiodbConn$deleteAllEntriesFromPersistentCache()biodb::BiodbConn$deleteAllEntriesFromVolatileCache()biodb::BiodbConn$deleteWholePersistentCache()biodb::BiodbConn$disallowEditing()biodb::BiodbConn$disallowWriting()biodb::BiodbConn$download()biodb::BiodbConn$editingIsAllowed()biodb::BiodbConn$filterEntriesOnRt()biodb::BiodbConn$getAllCacheEntries()biodb::BiodbConn$getAllVolatileCacheEntries()biodb::BiodbConn$getBiodb()biodb::BiodbConn$getCacheFile()biodb::BiodbConn$getCacheId()biodb::BiodbConn$getChromCol()biodb::BiodbConn$getDownloadPath()biodb::BiodbConn$getEntry()biodb::BiodbConn$getEntryContent()biodb::BiodbConn$getEntryContentFromDb()biodb::BiodbConn$getEntryContentRequest()biodb::BiodbConn$getEntryIds()biodb::BiodbConn$getEntryImageUrl()biodb::BiodbConn$getEntryPageUrl()biodb::BiodbConn$getId()biodb::BiodbConn$getMatchingMzField()biodb::BiodbConn$getMzValues()biodb::BiodbConn$getNbEntries()biodb::BiodbConn$getNbPeaks()biodb::BiodbConn$getSearchableFields()biodb::BiodbConn$initialize()biodb::BiodbConn$isCompounddb()biodb::BiodbConn$isDownloadable()biodb::BiodbConn$isDownloaded()biodb::BiodbConn$isEditable()biodb::BiodbConn$isExtracted()biodb::BiodbConn$isMassdb()biodb::BiodbConn$isRemotedb()biodb::BiodbConn$isSearchableByField()biodb::BiodbConn$isWritable()biodb::BiodbConn$makeRequest()biodb::BiodbConn$makesRefToEntry()biodb::BiodbConn$msmsSearch()biodb::BiodbConn$print()biodb::BiodbConn$requiresDownload()biodb::BiodbConn$searchByName()biodb::BiodbConn$searchCompound()biodb::BiodbConn$searchForEntries()biodb::BiodbConn$searchForMassSpectra()biodb::BiodbConn$searchMsEntries()biodb::BiodbConn$searchMsPeaks()biodb::BiodbConn$searchMzRange()biodb::BiodbConn$searchMzTol()biodb::BiodbConn$setDownloadedFile()biodb::BiodbConn$setEditingAllowed()biodb::BiodbConn$setMatchingMzField()biodb::BiodbConn$setWritingAllowed()biodb::BiodbConn$write()biodb::BiodbConn$writingIsAllowed()wsSearch()
Calls search service on the database for searching for compounds. See https://www.uniprot.org/help/programmatic_access for details.
UniprotConn$wsSearch(
query = "",
fields = NULL,
format = NULL,
size = NULL,
retfmt = c("plain", "parsed", "ids", "request")
)queryThe query to send to the database.
fieldsThe field columns to retrieve from the database (e.g.: 'id', 'entry name', 'pathway', 'organism', 'sequence', etc).
formatThe return format (e.g.: 'tsv').
sizeThe maximum number of entries to return.
retfmtUse to set the format of the returned value. 'plain' will return the raw results from the server, as a character value. 'parsed' will return the parsed results, as a JSON object. 'request' will return a BiodbRequest object representing the request as it would have been sent. 'ids' will return a character vector containing the IDs of the matching entries.
Depending on 'retfmt' parameter.
wsQuery()
Calls query service on the database for searching for compounds. See http //www.uniprot.org/help/api_queries for details.
UniprotConn$wsQuery(
query = "",
columns = NULL,
format = NULL,
limit = NULL,
retfmt = c("plain", "parsed", "ids", "request")
)queryThe query to send to the database.
columnsThe field columns to retrieve from the database (e.g.: 'id', 'entry name', 'pathway', 'organism', 'sequence', etc).
formatThe return format (e.g.: 'tsv').
limitThe maximum number of entries to return.
retfmtUse to set the format of the returned value. 'plain' will return the raw results from the server, as a character value. 'parsed' will return the parsed results, as a JSON object. 'request' will return a BiodbRequest object representing the request as it would have been sent. 'ids' will return a character vector containing the IDs of the matching entries.
Depending on 'retfmt' parameter.
geneSymbolToUniprotIds()
Gets UniProt IDs associated with gene symbols.
UniprotConn$geneSymbolToUniprotIds( genes, ignore.nonalphanum = FALSE, partial.match = FALSE, filtering = TRUE, max.results = 0 )
genesA vector of gene symbols to convert to UniProt IDs.
ignore.nonalphanumIf set to TRUE, do not take into account non-alphanumeric characters when comparing gene symbols.
partial.matchIf set to TRUE, a match will be valid even if the provided gene symbol is only a substring of the found gene symbol.
filteringIf set to FALSE, do not run any filtering and return all the UniProt IDs given by UniProt search web service. DEPRECATED: new UniProt REST API returns only exact match.
max.resultsMaximum of UniProt IDs returned for each gene symbol.
A named list of vectors of UniProt IDs. The names are gene symbols provided with the genes parameter. For each gene symbol, a vector of found UniProt IDs is set.
clone()
The objects of this class are cloneable with this method.
UniprotConn$clone(deep = FALSE)
deepWhether to make a deep clone.
# Create an instance with default settings: mybiodb <- biodb::newInst() # Get Uniprot connector uniprot <- mybiodb$getFactory()$createConn('uniprot') # Access web service "search": result <- uniprot$wsSearch(query='protein_name:"prion protein"', fields=c('id', 'entry name'), format='tsv', size=10) # Terminate instance. mybiodb$terminate()# Create an instance with default settings: mybiodb <- biodb::newInst() # Get Uniprot connector uniprot <- mybiodb$getFactory()$createConn('uniprot') # Access web service "search": result <- uniprot$wsSearch(query='protein_name:"prion protein"', fields=c('id', 'entry name'), format='tsv', size=10) # Terminate instance. mybiodb$terminate()
This is the entry class for Uniprot database.
biodb::BiodbEntry -> biodb::BiodbXmlEntry -> UniprotEntry
biodb::BiodbEntry$appendFieldValue()biodb::BiodbEntry$cloneInstance()biodb::BiodbEntry$computeFields()biodb::BiodbEntry$fieldHasBasicClass()biodb::BiodbEntry$getBiodb()biodb::BiodbEntry$getDbClass()biodb::BiodbEntry$getField()biodb::BiodbEntry$getFieldCardinality()biodb::BiodbEntry$getFieldClass()biodb::BiodbEntry$getFieldDef()biodb::BiodbEntry$getFieldNames()biodb::BiodbEntry$getFieldValue()biodb::BiodbEntry$getFieldsAsDataframe()biodb::BiodbEntry$getFieldsAsJson()biodb::BiodbEntry$getFieldsByType()biodb::BiodbEntry$getId()biodb::BiodbEntry$getName()biodb::BiodbEntry$getParent()biodb::BiodbEntry$hasField()biodb::BiodbEntry$isNew()biodb::BiodbEntry$makesRefToEntry()biodb::BiodbEntry$parentIsAConnector()biodb::BiodbEntry$parseContent()biodb::BiodbEntry$print()biodb::BiodbEntry$removeField()biodb::BiodbEntry$setField()biodb::BiodbEntry$setFieldValue()biodb::BiodbXmlEntry$initialize()clone()
The objects of this class are cloneable with this method.
UniprotEntry$clone(deep = FALSE)
deepWhether to make a deep clone.
# Create an instance with default settings: mybiodb <- biodb::newInst() # Create a connector conn <- mybiodb$getFactory()$createConn('uniprot') # Get an entry e <- conn$getEntry('P01011') # Terminate instance. mybiodb$terminate()# Create an instance with default settings: mybiodb <- biodb::newInst() # Create a connector conn <- mybiodb$getFactory()$createConn('uniprot') # Get an entry e <- conn$getEntry('P01011') # Terminate instance. mybiodb$terminate()