ChebiConn: ChEBI connector class.

In pkrog/biodbChebi: biodbChebi, a library for connecting to the ChEBI Database

ChEBI connector class.

Description

ChEBI connector class.

ChEBI connector class.

Details

This is the connector class for connecting to the ChEBI database through its web services.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> ChebiConn

Methods

Public methods

• ChebiConn$new()

• ChebiConn$wsWsdl()

• ChebiConn$wsGetLiteEntity()

• ChebiConn$convIdsToChebiIds()

• ChebiConn$convInchiToChebi()

• ChebiConn$convCasToChebi()

• ChebiConn$getWsdl()

• ChebiConn$getWsdlEnumeration()

• ChebiConn$getStarsCategories()

• ChebiConn$getSearchCategories()

• ChebiConn$clone()

Inherited methods

• 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$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()

---

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.

Usage

ChebiConn$new(...)

Arguments

...

All parameters are passed to the super class initializer.

Returns

Nothing.

---

Method wsWsdl()

Retrieves the complete WSDL from the web server.

Usage

ChebiConn$wsWsdl(retfmt = c("plain", "parsed", "request"))

Arguments

retfmt

The return format to use. 'plain' will return the value as it is returned by the server. 'parsed' will return an XML object. 'request' will return a BiodbRequest object representing the request that would have been sent.

Returns

Depending on 'retfmt' value.

---

Method wsGetLiteEntity()

Calls getLiteEntity web service and returns the XML result. Be careful when searching by mass (search.category='MASS' or 'MONOISOTOPIC MASS'), since the search is made in text mode, thus the number must be exactly written as it is stored in database, eventually padded with 0 in order to have exactly 5 digits after the decimal. An easy solution is to use wildcards to search a mass '410;.718*'. See http //www.ebi.ac.uk/chebi/webServices.do for more details.

Usage

ChebiConn$wsGetLiteEntity(
  search = NULL,
  search.category = "ALL",
  stars = "ALL",
  max.results = 10,
  retfmt = c("plain", "parsed", "request", "ids")
)

Arguments

search

The text or pattern to search.

search.category

The search category. Call 'getSearchCategories()' to get a full list of search categories.

stars

How many starts the returned entities should have. Call 'getStarsCategories() to get a full list of starts categories.'

max.results

The maximum of results to return.

retfmt

The return format to use. 'plain' will return the results as given by the server, in a string. 'parsed' will return an XML object. 'request' will return a BiodbRequest object representing the request as would have been sent. 'ids' will return a list of matched entity IDs.

Returns

Depending on 'retfmt' value.

---

Method convIdsToChebiIds()

Converts a list of IDs (InChI, InChI Keys, CAS, ...) into a list of ChEBI IDs. Several ChEBI IDs may be returned for a single ID.

Usage

ChebiConn$convIdsToChebiIds(ids, search.category, simplify = TRUE)

Arguments

ids

The identifiers to convert.

search.category

The search category. Call 'getSearchCategories()' to get a full list of search categories.

simplify

If set to TRUE and only one ChEBI ID has been found for each ID, then a character vector is returned. Otherwise a list of character vectors is returned.

Returns

Depending on the value of simplify.

---

Method convInchiToChebi()

Converts a list of InChI or InChI KEYs into a list of ChEBI IDs. Several ChEBI IDs may be returned for a single InChI or InChI KEY.

Usage

ChebiConn$convInchiToChebi(inchi, simplify = TRUE)

Arguments

inchi

The InChI values to convert.

simplify

If set to TRUE and only one ChEBI ID has been found for each ID, then a character vector is returned. Otherwise a list of character vectors is returned.

Returns

Depending on the value of simplify.

---

Method convCasToChebi()

Converts a list of CAS IDs into a list of ChEBI IDs. Several ChEBI IDs may be returned for a single InChI or InChI KEY.

Usage

ChebiConn$convCasToChebi(cas, simplify = TRUE)

Arguments

cas

The CAS IDs to convert.

simplify

If set to TRUE and only one ChEBI ID has been found for each ID, then a character vector is returned. Otherwise a list of character vectors is returned.

Returns

Depending on the value of simplify.

---

Method getWsdl()

Gets the WSDL as an XML object.

Usage

ChebiConn$getWsdl()

Returns

The ChEBI WSDL as an XML object.

---

Method getWsdlEnumeration()

Extracts a list of values from an enumeration in the WSDL.

Usage

ChebiConn$getWsdlEnumeration(name)

Arguments

name

The name of the enumeration for which to retrieve the values.

Returns

A character vector listing the enumerated values.

---

Method getStarsCategories()

Gets the list of allowed stars categories for the getLiteEntity web service.

Usage

ChebiConn$getStarsCategories()

Returns

Returns all the possible stars categories as a character vector.

---

Method getSearchCategories()

Gets the list of allowed search categories for the getLiteEntity web service.

Usage

ChebiConn$getSearchCategories()

Returns

Returns all the possible search categories as a character vector.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

ChebiConn$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Create a connector
conn <- mybiodb$getFactory()$createConn('chebi')

# Get an entry
e <- conn$getEntry('15440')

# Convert an InChI KEY to a ChEBI identifier
conn$convInchiToChebi('YYGNTYWPHWGJRM-AAJYLUCBSA-N')

# Terminate instance.
mybiodb$terminate()

pkrog/biodbChebi documentation built on March 29, 2022, 8:40 a.m.