reutils
reutils is an R package for interfacing with NCBI databases such as
PubMed, Genbank, or GEO via the Entrez Programming Utilities
(EUtils). It provides
access to the nine basic eutils: einfo, esearch, esummary,
epost, efetch, elink, egquery, espell, and ecitmatch.
Please check the relevant usage guidelines when using these services. Note that Entrez server requests are subject to frequency limits. Consider obtaining an NCBI API key if are a heavy user of E-utilities.
Installation
You can install the released version of reutils from CRAN with:
install.packages("reutils")Install the development version from github using the devtools
package.
require("devtools")
install_github("gschofl/reutils")Please post feature or support requests and bugs at the issues tracker for the reutils package on GitHub.
Important functions
With nine E-Utilities, NCBI provides a programmatical interface to the Entrez query and database system for searching and retrieving requested data
Each of these tools corresponds to an R function in the reutils
package described below.
esearch
esearch: search and retrieve a list of primary UIDs or the NCBI
History Server information (queryKey and webEnv). The objects returned
by esearch can be passed on directly to epost, esummary, elink,
or efetch.
efetch
efetch: retrieve data records from NCBI in a specified retrieval type
and retrieval mode as given in this
table.
Data are returned as XML or text documents.
esummary
esummary: retrieve Entrez database summaries (DocSums) from a list of
primary UIDs (Provided as a character vector or as an esearch object)
elink
elink: retrieve a list of UIDs (and relevancy scores) from a target
database that are related to a set of UIDs provided by the user. The
objects returned by elink can be passed on directly to epost,
esummary, or efetch.
einfo
einfo: provide field names, term counts, last update, and available
updates for each database.
epost
epost: upload primary UIDs to the users’s Web Environment on the
Entrez history server for subsequent use with esummary, elink, or
efetch.
Examples
esearch: Searching the Entrez databases
Let’s search PubMed for articles with Chlamydia psittaci in the title that have been published in 2013 and retrieve a list of PubMed IDs (PMIDs).
pmid <- esearch("Chlamydia psittaci[titl] and 2013[pdat]", "pubmed")
pmid
#> Object of class 'esearch'
#> List of UIDs from the 'pubmed' database.
#> [1] "24689181" "24326117" "24324029" "24273177" "24163776" "23699067"
#> [7] "23691148" "23654298" "23532978" "23405306" "23391180" "23318575"
#> [13] "26623327" "23265868" "23227890" "23098816"Alternatively we can collect the PMIDs on the history server.
pmid2 <- esearch("Chlamydia psittaci[titl] and 2013[pdat]", "pubmed", usehistory = TRUE)
pmid2
#> Object of class 'esearch'
#> Web Environment for the 'pubmed' database.
#> Number of UIDs stored on the History server: 16
#> Query Key: 1
#> WebEnv: MCID_5f7f350855fd2846091d0624We can also use esearch to search GenBank. Here we do a search for
polymorphic membrane proteins (PMPs) in Chlamydiaceae.
cpaf <- esearch("Chlamydiaceae[orgn] and PMP[gene]", "nucleotide")
cpaf
#> Object of class 'esearch'
#> List of UIDs from the 'nucleotide' database.
#> [1] "519865230" "410810883" "313847556" "532821947" "519796743" "532821218"
#> [7] "519794601"Some accessors for esearch objects
getUrl(cpaf)
#> [1] "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?term=Chlamydiaceae%5Borgn%5D%20AND%20PMP%5Bgene%5D&db=nucleotide&retstart=0&retmax=100&rettype=uilist&retmode=xml&email=gerhard.schofl%40gmail.com&tool=reutils"getError(cpaf)
#> No errorsdatabase(cpaf)
#> [1] "nucleotide"Extract a vector of GIs:
uid(cpaf)
#> [1] "519865230" "410810883" "313847556" "532821947" "519796743" "532821218"
#> [7] "519794601"Get query key and web environment:
querykey(pmid2)
#> [1] 1webenv(pmid2)
#> [1] "MCID_5f7f350855fd2846091d0624"Extract the content of an EUtil request as XML.
content(cpaf, "xml")
#> <?xml version="1.0" encoding="UTF-8"?>
#> <!DOCTYPE eSearchResult PUBLIC "-//NLM//DTD esearch 20060628//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20060628/esearch.dtd">
#> <eSearchResult>
#> <Count>7</Count>
#> <RetMax>7</RetMax>
#> <RetStart>0</RetStart>
#> <IdList>
#> <Id>519865230</Id>
#> <Id>410810883</Id>
#> <Id>313847556</Id>
#> <Id>532821947</Id>
#> <Id>519796743</Id>
#> <Id>532821218</Id>
#> <Id>519794601</Id>
#> </IdList>
#> <TranslationSet>
#> <Translation>
#> <From>Chlamydiaceae[orgn]</From>
#> <To>"Chlamydiaceae"[Organism]</To>
#> </Translation>
#> </TranslationSet>
#> <TranslationStack>
#> <TermSet>
#> <Term>"Chlamydiaceae"[Organism]</Term>
#> <Field>Organism</Field>
#> <Count>119488</Count>
#> <Explode>Y</Explode>
#> </TermSet>
#> <TermSet>
#> <Term>PMP[gene]</Term>
#> <Field>gene</Field>
#> <Count>63</Count>
#> <Explode>N</Explode>
#> </TermSet>
#> <OP>AND</OP>
#> </TranslationStack>
#> <QueryTranslation>"Chlamydiaceae"[Organism] AND PMP[gene]</QueryTranslation>
#> </eSearchResult>
#> Or extract parts of the XML data using the reference class method
#xmlValue() and an XPath expression:
cpaf$xmlValue("//Id")
#> [1] "519865230" "410810883" "313847556" "532821947" "519796743" "532821218"
#> [7] "519794601"esummary: Retrieving summaries from primary IDs
esummary retrieves document summaries (docsums) from a list of
primary IDs. Let’s find out what the first entry for PMP is about:
esum <- esummary(cpaf[1])
esum
#> Object of class 'esummary'
#> <?xml version="1.0" encoding="UTF-8"?>
#> <!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD esummary nuccore 20190808//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20190808/esummary_nuccore.dtd">
#> <eSummaryResult>
#> <DocumentSummarySet status="OK">
#> <DocumentSummary uid="519865230">
#> <Caption>KE360863</Caption>
#> <Title>Chlamydia psittaci 84-8471/1 genomic scaffold CP_84_8471_1.contig.1261, whole genome shotgun sequence</Title>
#> <Extra>gi|519865230|gnl|WGS:ATMY01|CP_84_8471_1.contig.1261|gb|KE360863.1|</Extra>
#> <Gi>519865230</Gi>
#> <CreateDate>2013/07/02</CreateDate>
#> <UpdateDate>2015/03/22</UpdateDate>
#> <Flags>32</Flags>
#> <TaxId>1112230</TaxId>
#> <Slen>255</Slen>
#> <Biomol>genomic</Biomol>
#> <MolType>dna</MolType>
#> <Topology>linear</Topology>
#> <SourceDb>insd</SourceDb>
#> <SegSetSize>0</SegSetSize>
#> <ProjectId>77033</ProjectId>
#> <Genome>genomic</Genome>
#> <SubType>strain|host|country</SubType>
#> <SubName>84-8471/1|Psittacidae|France</SubName>
...We can also parse docsums into a tibble
esum <- esummary(cpaf[1:4])
content(esum, "parsed")
#> # A tibble: 4 x 32
#> Id Caption Title Extra Gi CreateDate UpdateDate Flags TaxId Slen Biomol
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 5198… KE3608… Chla… gi|5… 5198… 2013/07/02 2015/03/22 32 1112… 255 genom…
#> 2 4108… HF5456… Chla… gi|4… 4108… 2012/11/05 2015/02/27 256 1221… 1171… genom…
#> 3 3138… FQ4821… Chla… gi|3… 3138… 2010/12/09 2015/02/27 256 9295… 1164… genom…
#> 4 5328… APJW00… Chla… gi|5… 5328… 2013/08/26 2013/12/30 0 1046… 4 genom…
#> # … with 21 more variables: MolType <chr>, Topology <chr>, SourceDb <chr>,
#> # SegSetSize <chr>, ProjectId <chr>, Genome <chr>, SubType <chr>,
#> # SubName <chr>, AssemblyGi <chr>, AssemblyAcc <chr>, Tech <chr>,
#> # Completeness <chr>, GeneticCode <chr>, Strand <chr>, Organism <chr>,
#> # Strain <chr>, BioSample <chr>, Statistics <chr>, Properties <chr>,
#> # OSLT <chr>, AccessionVersion <chr>efetch: Downloading full records from Entrez
First we search the protein database for sequences of the chlamydial protease activity factor, CPAF
cpaf <- esearch("Chlamydia[orgn] and CPAF", "protein")
cpaf
#> Object of class 'esearch'
#> List of UIDs from the 'protein' database.
#> [1] "1740844119" "1690612929" "1690612140" "1590752519" "1468362670"
#> [6] "1390541316" "1388009003" "1304476351" "1205197358" "1205197013"
#> [11] "1196960997" "1167830407" "1167829710" "1167819646" "1167812968"
#> [16] "1167811336" "1167810779" "1167809436" "1167808506" "1150780591"
#> [21] "1096224813" "1054715832" "970511880 " "763061928 " "737425953 "
#> [26] "695827004 " "657885234 " "566141963 " "546198781 " "545649479 "
#> [31] "545648761 " "520984156 " "520949412 " "504759924 " "504757682 "
#> [36] "504756587 " "504330504 " "503477904 " "503227943 " "499777634 "
#> [41] "499438719 " "499409418 " "499315665 " "499185655 " "497917205 "
#> [46] "1853088090" "1853087101" "1853085802" "1853084898" "497558476 "
#> [51] "497557614 " "505318867 " "497558952 " "503750877 " "1796080860"
#> [56] "1779221650" "1740844407" "1735479057" "1590752124" "527331510 "
#> [61] "504354663 " "502187753 " "497559629 " "497558818 " "1691271235"
#> [66] "1690613258" "1690611733" "1176345240" "1167810032" "566141881 "
#> [71] "1167820103" "1167812907" "1167811317" "1150780450" "504760124 "
#> [76] "504757474 " "504330993 " "503477468 " "1167819613" "1167813646"
#> [81] "1167812055" "545649834 " "520983701 " "504756851 " "499316208 "
#> [86] "497558063 " "1176351765" "1167830589" "566141274 " "546198309 "
#> [91] "504759730 " "499194655 " "1468363373" "1388009422" "1304475903"
#> [96] "1167814130" "1167809415" "1054716803" "737427177 " "545649179 "Let’s fetch the FASTA record for the first protein. To do that, we have
to set rettype = "fasta" and retmode = "text":
cpaff <- efetch(cpaf[1], rettype = "fasta", retmode = "text")
cpaff
#> Object of class 'efetch'
#> >WP_149305081.1 outer membrane complex protein OmcB [Chlamydia abortus]
#> MSKLIRRVVTVLALTSMASSFASGKIEAAAAESLATRFIASTENSNDNVLQATAKKVRFGRNKNQRQEQK
#> HTGAFCDKEFYPCEGGQCQSVDTTQESCYGKMYCVRVNDDCNVEISQAVPEYATVGSPYPIEILAVGKKD
#> CVNVVITQQLPCEVEFVSSDPATTPTSDSKLIWTIDRLGQGEKCKITVWVKPLKEGCCFTAATVCACPEL
#> RSYTKCGQPAICIKQEGPECACLRCPVCYKIEVCNTGSAIARNVVVDNPVPDGYTHASGQRVLSFNLGDM
#> RPGDSKCFSVEFCPQKRGKITNVATVSYCGGHKCSANVTTVVNEPCVQVNISGADWSYVCKPVEYTIVVS
#> NPGDLKLYDVVVEDTAPSGATILEAEGAEICCNKAVWCIKEMCPGETLQFKVVAKAQSPGKFTNQVVVKT
#> NSDCGTCTSCAEATTHWKGLAATHMCVIDTNDPICVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPV
#> SSSGPTKGTITGNTVVFDALPKLGSKESVEFSVTLKGIAPGDARGEAILSSDTLTVPVADTENTHVY
#>
#>
#> ...
#> EFetch query using the 'protein' database.
#> Query url: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?=efe...'
#> Retrieval type: 'fasta', retrieval mode: 'text'Now we can write the sequence to a fasta file by first extracting the
data from the efetch object using content():
write(content(cpaff), file = "~/cpaf.fna")cpafx <- efetch(cpaf, rettype = "fasta", retmode = "xml")
cpafx
#> Object of class 'efetch'
#> <?xml version="1.0" encoding="UTF-8"?>
#> <!DOCTYPE TSeqSet PUBLIC "-//NCBI//NCBI TSeq/EN" "https://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.dtd">
#> <TSeqSet>
#> <TSeq>
#> <TSeq_seqtype value="protein"/>
#> <TSeq_accver>WP_149305081.1</TSeq_accver>
#> <TSeq_taxid>83555</TSeq_taxid>
#> <TSeq_orgname>Chlamydia abortus</TSeq_orgname>
#> <TSeq_defline>outer membrane complex protein OmcB [Chlamydia abortus]</TSeq_defline>
#> <TSeq_length>557</TSeq_length>
#> <TSeq_sequence>MSKLIRRVVTVLALTSMASSFASGKIEAAAAESLATRFIASTENSNDNVLQATAKKVRFGRNKNQRQEQKHTGAFCDKEFYPCEGGQCQSVDTTQESCYGKMYCVRVNDDCNVEISQAVPEYATVGSPYPIEILAVGKKDCVNVVITQQLPCEVEFVSSDPATTPTSDSKLIWTIDRLGQGEKCKITVWVKPLKEGCCFTAATVCACPELRSYTKCGQPAICIKQEGPECACLRCPVCYKIEVCNTGSAIARNVVVDNPVPDGYTHASGQRVLSFNLGDMRPGDSKCFSVEFCPQKRGKITNVATVSYCGGHKCSANVTTVVNEPCVQVNISGADWSYVCKPVEYTIVVSNPGDLKLYDVVVEDTAPSGATILEAEGAEICCNKAVWCIKEMCPGETLQFKVVAKAQSPGKFTNQVVVKTNSDCGTCTSCAEATTHWKGLAATHMCVIDTNDPICVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSSSGPTKGTITGNTVVFDALPKLGSKESVEFSVTLKGIAPGDARGEAILSSDTLTVPVADTENTHVY</TSeq_sequence>
#> </TSeq>
#> <TSeq>
#> <TSeq_seqtype value="protein"/>
#> <TSeq_accver>WP_139414852.1</TSeq_accver>
#> <TSeq_taxid>83555</TSeq_taxid>
#> <TSeq_orgname>Chlamydia abortus</TSeq_orgname>
#> <TSeq_defline>outer membrane complex protein OmcB [Chlamydia abortus]</TSeq_defline>
#> <TSeq_length>557</TSeq_length>
#> <TSeq_sequence>MSKLIRRVVTVLALTSMASSFASGKIEAAAAESLATRFIASTENSNDNVLQATAKKVRFGRNKNQRQEQKHTGAFCDKEFYPCEGGQCQSVDTTQESCYGKMYCVRVNDDCNVEISQAVPEYATVGSPYPIEILAVGKKDCVNVVITQQLPCEVEFVSSDPATTPTSDSKLIWTIDRLGQGEKCKITVWVKPLKEGCCFTAATVCACPELRSYTKCGQPAICIKQEGPECACLRCPVCYKIEVCNTGSAIARNVVVDNPVPDGYTHASGQRVLSFNLGDMRPGDSKCFSVEFCPQKRGKITNVATVSYCGGHKCSANVTTVVNEPCVQVNISGVDWSYVCKPVEYTIVVSNPGDLKLYDVVVEDTAPSGATILEAEGAEICCNKAVWCIKEMCPGETLQFKVVAKAQSPGKFTNQVVVKTNSDCGTCTSCAEATTHWKGLAATHMCVIDTNDPICVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSSSGPTKGTITGNTVVFDALPKLGSKESVEFSVTLKGIAPGDARGEAILSSDTLTVPVADTENTHVY</TSeq_sequence>
#> </TSeq>
#> <TSeq>
#> <TSeq_seqtype value="protein"/>
...aa <- cpafx$xmlValue("//TSeq_sequence")
aa
#> [1] "MSKLIRRVVTVLALTSMASSFASGKIEAAAAESLATRFIASTENSNDNVLQATAKKVRFGRNKNQRQEQKHTGAFCDKEFYPCEGGQCQSVDTTQESCYGKMYCVRVNDDCNVEISQAVPEYATVGSPYPIEILAVGKKDCVNVVITQQLPCEVEFVSSDPATTPTSDSKLIWTIDRLGQGEKCKITVWVKPLKEGCCFTAATVCACPELRSYTKCGQPAICIKQEGPECACLRCPVCYKIEVCNTGSAIARNVVVDNPVPDGYTHASGQRVLSFNLGDMRPGDSKCFSVEFCPQKRGKITNVATVSYCGGHKCSANVTTVVNEPCVQVNISGADWSYVCKPVEYTIVVSNPGDLKLYDVVVEDTAPSGATILEAEGAEICCNKAVWCIKEMCPGETLQFKVVAKAQSPGKFTNQVVVKTNSDCGTCTSCAEATTHWKGLAATHMCVIDTNDPICVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSSSGPTKGTITGNTVVFDALPKLGSKESVEFSVTLKGIAPGDARGEAILSSDTLTVPVADTENTHVY"
#> [2] "MSKLIRRVVTVLALTSMASSFASGKIEAAAAESLATRFIASTENSNDNVLQATAKKVRFGRNKNQRQEQKHTGAFCDKEFYPCEGGQCQSVDTTQESCYGKMYCVRVNDDCNVEISQAVPEYATVGSPYPIEILAVGKKDCVNVVITQQLPCEVEFVSSDPATTPTSDSKLIWTIDRLGQGEKCKITVWVKPLKEGCCFTAATVCACPELRSYTKCGQPAICIKQEGPECACLRCPVCYKIEVCNTGSAIARNVVVDNPVPDGYTHASGQRVLSFNLGDMRPGDSKCFSVEFCPQKRGKITNVATVSYCGGHKCSANVTTVVNEPCVQVNISGVDWSYVCKPVEYTIVVSNPGDLKLYDVVVEDTAPSGATILEAEGAEICCNKAVWCIKEMCPGETLQFKVVAKAQSPGKFTNQVVVKTNSDCGTCTSCAEATTHWKGLAATHMCVIDTNDPICVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSSSGPTKGTITGNTVVFDALPKLGSKESVEFSVTLKGIAPGDARGEAILSSDTLTVPVADTENTHVY"
#> [3] "MSKLIRRVVTVLALTSMASSFASGKIEAAAAESLATRFIASTENSNDNVLQATAKKVRFGRNKNQRQEQKHTGAFCDKEFYPCEGGQCQSVDTTQESCYGKMYCVRVNDDCNVEISQAVPEYATVGSPYPIEILAVGKKDCVNVVITQQLPCEVEFVSSDPATTPTSDSKLIWTIDRLGQGEKCKITVWVKPLKEGCCFTAATVCACPELRSYTKCGQPAICIKQEGPECACLRCPVCYKIEVCNTGSAIARNVVVDNPVPDGYTHASGQRVLSFNLGDMRPGDSKCFSVEFCPQKRGKINNVATVSYCGGHKCSANVTTVVNEPCVQVNISGADWSYVCKPVEYTIVVSNPGDLKLYDVVVEDTAPSGATILEADGAEICCNKAVWCIKEMYPGETLQFKVVAKAQSPGKFTNQVVVKTNSDCGTCTSCAEATTHWKGLAATHMCVIDTNDPICLGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSSSGPTKGTITGNTVVFDALPKLGSKESVEFSVTLKGIAPGDARGEAILSSDTLTVPVADTENTHVY"
#> [4] "MSKLIRRVVTVLALTSMASSFASGKIEAAAAESLATRFIASTENSDDNVLQTTAKKVRFGRNKNQRQEQKHTGAFCDKEFYPCEGGQCQSVDTTQESCYGKMYCVRVNDDCNVEISQAVPEYATVGSPYPIEILAVGKKDCVNVVITQQLPCEVEFVSSDPATTPTSDSKLIWTIDRLGQGEKCKITVWVKPLKEGCCFTAATVCACPELRSYTKCGQPAICIKQEGPECACLRCPVCYKIEVCNTGSAIARNVVVDNPVPDGYTHASGQRVLSFNLGDMRPGDSKCFCVEFCPQKRGKVTNVATVSYCGGHKCSSNVTTVVNEPCVQVNISGADWSYVCKPVEYTIVVSNPGDLKLYDVVIEDTAPSGATILEAAGAEICCNKAVWCIKEMCPGETLQFKVVAKAQSPGKFTNQVVVKTNSDCGTCTSCAEATTHWKGLAATHMCVIDTNDPICVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSSSGPTKGTITGNTVVFDALPKLGSKESVEFSVTLKGIAPGDARGEAILSSDTLTVPVADTENTHVY"
#> [5] "MSKLIRRVVTVLALTSMASSFASGKIEAAAAESLATRFIASADNSDDNILQTTAKKVRFGRNKNQKQEQKNNSPCCDKEFYPCQDGSCQSSVDTKQESCYGKMYCIRVNDDCNVEISQAVPEYATVGSPYPIEILAVGKKDCVNVVITQQLPCEVEFVSSDPVTTPTSDSKLIWTIDRLSQGEKCKITVWVKPLKEGCCFTAATVCACPELRSYTKCGQPAICIKQEGPDCACLRCPVCYKIEVCNTGSAVARGVVVDNPVPDGYTHASGQRVLSFNLGDMRPGDFKSFTVEFCPQKRGKVTNVATVSYCGGHKCSANVTTVINEPCVQVNISGADWSYVCKPVEYTIVVSNPGDLKLYDVVIEDTTPSGATILEAAGAEICCNKAVWCIKEMCPGETLQFKIVAKAQNPGKFTNQVSVRTNSDCGSCTSCAEVTTHWKGLAATHMCVIDTNDPICVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSSSGPTKGTITGNTVVFDALPKLGSKESVEFSVTLKGVAPGDARGEAILSSDTLTVPVADTENTHVY"
#> [6] "MRIGDPMNKLIRRAVTIFAVTSVASLFASGVLETSMAESLSTNVISLADTKAKNTASHHKDKKARKNHQKETPVVHNQAVAPVRESKSTGPKQDSCFGKMYTVKVNDDRNVEITQSVPEYATVGSPYPIEITAKGKRDCVDVIITQQLPCEAEFVSSDPATTPTADGKLVWKIDRLGQGEESKITVWVKPLKEGCCFTAATVCACPEIRSVTKCGQPAICVKQEGPECACLRCPVTYKILVTNQGTATARNVVLENPVPDGFAHSSGQRVLTYTLGDMQPGEQKVVTVEFCPLKRGRATNIATVSYCGGHKNTASVTTVINEPCVQVNIAGADWSYVCKPVEYVISVSNPGDLILRDVVVEDTLSPGVTVIEAPGAQISCNKVVWTVKELNPGESLQYKVLVRAQTPGQFTNNVVVKSCSDCGTCTSCAEATTYWKGVAATHMCVVDTCDPVCVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSFSGPTKGTITGNTVVFDALPRLGSKETVEFSVTLKAVSAGDARGEAILSSDTLTVPVSDTENTHIY"
#> [7] "MSKLIRRVVTVLALTSMASCFASGGIEAAVAESLITKIVASAETKPAPVPVTAKKVRLVRKNKQPVEQNSRGAFCDKEFYPCEEGRGCQPLEAQQESCYGRLYSVKVNDDCNVEICQSVPEYATVGSPYPIEILAIGKKDCVDVVITQQLPCEAEFVSSDPETVPTNDGKLIWKIDRLGQGDRCKITVWVKPLKEGCCFTAATVCACPELRSYTKCGQPAICIKQEGPECACLRCPVCYKIEVVNTGSAIARNVTVDNPVPDGYSHASGQRVLSFNLGDMKPGDKKVFAVEFCPQKRGQVTNIATVTYCGGHKCSASVTTIVNEPCVQVNISGADWSYVCKPVEYAISVSNPGDLILHDVVIQDNLPSGVTVLEAPGGEICCNKVVWRIKEMCPGETLQFKVVVKAQVPGRFTNQVAVTSQSDCGSCTCCAEATTHWKGLAATHMCVLDTNDPICVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPIASSGPTKGTISGNTVVFDALPKLGSKESVEFSVTLKGIAPGDARGEAILSSDTLTSPVSDTENTHVY"
#> [8] "MSKLIRRVVTVLALTSMASCFASGGIEAAVAESLITKIVASAERQPAPVPVTAKKVRLVRKNKQPVEQKSRGAFCDKEFYPCEEGRCQPLEAQQESCYGRLYSVKVNDDCNVEICQSVPEYATVGSPYPIEILAIGKKDCVDVVITQQLPCEAEFVSSDPETTPTSDGKLIWKIDRLGQGDKCKIAVWVKPLKEGCCFTAATVCACPELRSYTKCGQPAVCIKQEGPECACLRCPVCYKIEVVNTGSATARNVTVDNPVPDGYSHASGQRVLSFNLGDMRPGDKKVFTVEFCPQRRGQVTNVATVTYCGGHKCSANVTTIVNEPCVQVNISGADWSYVCKPVEYSISVSNPGDLVLHDVVIQDNLPSGVTLIEAPGGEICCNKVVWRIKEMCPGETLQFKLLVKAQVPGRFTNQVAVTSESNCGTCTCCADATTHWKGLAATHMCVLDTNDPICVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVASSGPTKGTISGNTVVFDALPKLGSKESVEFSVTLKGIAPGDARGEAILSSDTLTSPVSDTENTHVY"
#> [9] "MRIGDPMNKLIRRAVTIFAVTSVASLFASGVLETSMAESLSTNVISLADTKAKNTASHHKDKKARKNHQKETPVVHNQAVAPVRESKSTGPKQDSCFGKMYTVKVNDDRNVEITQSVPEYATVGSPYPIEITAKGKRDCVDVIITQQLPCEAEFVSSDPATTPTADGKLVWKIDRLGQGEESKITVWVKPLKEGCCFTAATVCACPEIRSVTKCGQPAICVKQEGPECACLRCPVTYKIHVVNQGTATARNVVLENPVPDGFAHSSGQRVLTYTLGDMQPGEQKVVTVEFCPLKRGRATNIATVSYCGGHKNTASVTTVINEPCVQVNIAGADWSYVCKPVEYVISVSNPGDLILRDVVVEDTLSPGVTVIEAPGAQISCNKVVWTVKELNPGESLQYKVLVRAQTPGQFTNNVVVKSCSDCGTCTSCAEATTYWKGVAATHMCVVDTCDPVCVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSFSGPTKGTITGNTVVFDALPRLGSKETVEFSVTLKAVSAGDARGEAILSSDTLTVPVSDTENTHIY"
#> [10] "MRIGDPMNKLIRRAVTIFAVTSVASLFASGVLETSMAESLSTNVISLADTKAKNTASHHKDKKARKNHQKETPVVHNQAVAPVRESKSTGPKQDSCFGKMYTVKVNDDRNVEITQSVPEYATVGSPYPIEITAKGKRDCVDVIITQQLPCEAEFVSSDPATTPTADGKLVWKIDRLGQGEESKITVWVKPLKEGCCFTAATVCACPEIRSVTKCGQPAICVKQEGPECACLRCPVTYKILVVNQGTATARNVVLENPVPDGFAHSSGQRVLTYTLGDMQPGEQKVVTVEFCPLKRGRATNIATVSYCGGHKNTASVTTVINEPCVQVNIAGADWSYVCKPVEYVISVSNPGDLILRDVVVEDTLSPGVTVIEAPGAQISCNKVVWTVKELNPGESLQYKVLVRAQTPGQFTNNVVVKSCSDCGTCTSCAEATTYWKGVAATHMCVVDTCDPVCVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSFSGPTKGTITGNTVVFDALPRLGSKETVEFSVTLKAVSAGDARGEAILSSDTLTVPVSDTENTHIY"
#> [11] "MSKLIRRVVTVLALTSMASSFASGKIEAAAAESLATRFIASTENSNDNVLQATAKKVRFGRNKNQRQEQKHTGAFCDKEFYPCEGGQCQSVDTTQESCYGKMYCVRVNDDCNVEISQAVPEYATVGSPYPIEILAVGKKDCVNVVITQQLPCEVEFVSSDPATTPTSDSKLIWTIDCLGQGEKCKITVWVKPLKEGCCFTAATVCACPELRSYTKCGQPAICIKQEGPECACLRCPVCYKIEVCNTGSAIARNVVVDNPVPDGYTHASGQRVLSFNLGDMRPGDSKCFSVEFCPQKRGKITNVATVSYCGGHKCSANVTTVVNEPCVQVNISGADWSYVCKPVEYTIVVSNLGDLKLYDVVVEDTVPSGATILEAEGAEICCNKAVWCIKEMCSGETLQFKVVAKAQSPGKFTNQVVVKTNSDCGTCTSCAEATTHWKGLAATHMCVIDTNDPICVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSSSGPTKGTITGNTVVFDALPKLGSKESVEFSVTLKGIAPGDARGEAILSSDTLTVPVADTENTHVY"
#> [12] "MNKLIRRAVTIFAVTSVASLFASGVLETSMAESLSTNVISLADTKAKNTASHHKDKKARKNHQKETPVVHNQAVAPVRESKSTGPKQDSCFGKMYTVKVNDDRNVEITQSVPEYATVGSPYPIEITAKGKRDCVDVIITQQLPCEAEFVSSDPATTPTADGKLVWKIDRLGQGETSKITVWVKPLKEGCCFTAATVCACPEIRSVTKCGQPAICVKQEGPECACLRCPVTYKIHVVNQGTATARNVVLENPVPDGFAHTSGQRVLTYTLGDMQPGEQKVITVEFCPLKRGRATNIATVSYCGGHKNTASVTTVINEPCVQVNIAGADWSYVCKPVEYVISVSNPGDLILRDVVVEDTLSPGVTVIEAPGAQISCNKVVWTVKELNPGESLQYKVLVRAQTPGQFTNNVVVKSCSDCGTCTSCAEATTYWKGVAATHMCVVDTCDPVCVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSFSGPTKGTITGNTVVFDALPRLGSKETVEFSVTLKAVSAGDARGEAILSSDTLTVPVSDTENTHIY"
#> [13] "MNKLIRRAVTIFAVTSVASLFASGVLETSMAESLSTNVISLADTKARNNAASHHKDKKARKNHQKETLVVHNQAVAPVRESKSTGLKQDSCFGRMYTVKVNDDRNVEITQAVPEYATVGSPYPIEITAKGKRDCVDVIITQQLPCEAEFVSSDPATTPTADGKLVWKIDRLGQGETSKITVWVKPLKEGCCFTAATVCACPEIRSVTKCGQPAICVKQEGPECACLRCPVTYKIHVINQGTATARNVVLENPVPDGFAHTSGQRVLTYTLGDMQPGEQKVITVEFCPLKRGRATNIATVSYCGGHKNTASVTTVINEPCVQVNIAGADWSYVCKPVEYVISVSNPGDLILRDVVVEDTLSPGVTVIEAPGAQISCNKVVWTVKELNPGESLQYKVLVRAQTPGQFTNNVVVKSCSDCGTCTSCAEATTYWKGVAATHMCVVDTCDPVCVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSFSGPTKGTITGNTVVFDALPRLGSKETVEFSVTLKAVSAGDARGEAILSSDTLTVPVSDTENTHIY"
#> [14] "MNKLIRRAVTIFAVTSVASLFASGVLETSMAESLSTNVISLADTKAKNTASHHKDKKARKNHQKETPVVHNQAVAPVRESKSTGPKQDSCFGKMYTVKVNDDRNVEITQSVPEYATVGSPYPIEITAKGKRDCVDVIITQQLPCEAEFVSSDPATTPTADGKLVWKIDRLGQGEESKITVWVKPLKEGCCFTAATVCACPEIRSVTKCGQPAICVKQEGPECACLRCPVTYKIHVVNQGTATARNVVLENPVPDGFAHSSGQRVLTYTLGDMQPGEQKVVTIEFCPLKRGRATNIATVSYCGGHKNTASVTTVINEPCVQVNIAGADWSYVCKPVEYVISVSNPGDLILRDVVVEDTLSPGVTVIEAPGAQISCNKVVWTVKELNPGESLQYKVLVRAQTPGQFTNNVVVKSCSDCGTCTSCAEATTYWKGVAATHMCVVDTCDPVCVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSFSGPTKGTITGNTVVFDALPRLGSKETVEFSVTLKAVSAGDARGEAILSSDTLTVPVSDTENTHIY"
#> [15] "MSKLIRRVVTVLALTSMASSFASGKIEAAAAESLATRFIASTENSNDNVLQATAKKVRFGRNKNQRQEQKHTGAFCDKEFYPCEGGQCQSVDTTQESCYGKMYCVRVNDDCNVEISQAVPEYATVGSPYPIEILAVGKKDCVNVVITQQLPCEVEFVSSDPATTPTSDSKLIWTIDRLGQGEKCKITVWVKPLKEGCCFTAATVCACPELRSYTKCGQPAICIKQEGPECACLRCPVCYKIEVCNTGSAIARNVVVDNPVPDGYTHASGQRVLSFNLGDMRPGDSKCFSVEFCPQKRGKITNVATVSYCGGHKCSANVTTVVNEPCVQVNISGADWSYVCKPVEYTIVVSNLGDLKLYDVVVEDTAPSGATILEAEGAEICCNKAVWCIKEMCSGETLQFKVVAKAQSPGKFTNQVVVKTNSDCGTCTSCAEATTHWKGLAATHMCVIDTNDPICVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSSSGPTKGTITGNTVVFDALPKLGSKESVEFSVTLKGIAPGDARGEAILSSDTLTVPVADTENTHVY"
#> [16] "MNKLIRRAVTIFAVTSVASLFASGVLETSMAESLSTNVISLADTKAKNTASHHKDKKARKNHQKETPVVHNQAVAPVRESKSTGPKQDSCFGKMYTVKVNDDRNVEITQSVPEYATVGSPYPIEITAKGKRDCVDVIITQQLPCEAEFVSSDPATTPTADGKLVWKIDRLGQGEESKITVWVKPLKEGCCFTAATVCACPEIRSVTKCGQPAICVKQEGPECACLRCPVTYKILVVNQGTATARNVVLENPVPDGFAHSSGQRVLTYTLGDMQPGEQKVVTVEFCPLKRGRATNIATVSYCGGHKNTASVTTVINEPCVQVNIAGADWSYVCKPVEYVISVSNPGDLILRDVVVEDTLSPGVTVIEAPGAQISCNKVVWTVKELNPGESLQYKVLVRAQTPGQFTNNVVVKSCSDCGTCTSCAEATTYWKGVAATHMCVVDTCDPVCVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSFSGPTKGTITGNTVVFDALPRLGSKETVEFSVTLKAVSAGDARGEAILSSDTLTVPVSDTENTHIY"
#> [17] "MNKLIRRAVTIFAVTSVASLFASGVLETSMAESLSTNVISLADTKAKNTASHHKDKKARKNHQKETPVVHNQAGAPVRESKSTGPKQDSCFGKMYTVKVNDDRNVEITQSVPEYATVGSPYPIEITAKGKRDCVDVIITQQLPCEAEFVSSDPATTPTADGKLVWKIDRLGQGEESKITVWVKPLKEGCCFTAATVCACPEIRSVTKCGQPAICVKQEGPECACLRCPVTYKIHVVNQGTATARNVVLENPVPDGFAHSSGQRVLTYTLGDMQPGEQKVVTIEFCPLKRGRATNIATVSYCGGHKNTASVTTVINEPCVQVNIAGADWSYVCKPVEYVISVSNPGDLILRDVVVEDTLSPGVTVIEAPGAQISCNKVVWTVKELNPGESLQYKVLVRAQTPGQFTNNVVVKSCSDCGTCTSCAEATTYWKGVAATHMCVVDTCDPVCVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSFSGPTKGTITGNTVVFDALPRLGSKETVEFSVTLKAVSAGDARGEAILSSDTLTVPVSDTENTHIY"
#> [18] "MNKLIRRAVTIFAVTSVASLFASGVLETSMAESLSTNVISLADTKARNTASHHKDKKARKNHQKETLVVHNQAVAPVRESKSTGLKQDSCFGRMYTVKVNDDRNVEITQAVPEYATVGSPYPIEITAKGKRDCVDVIITQQLPCEAEFVSSDPATTPTADGKLVWKIDRLGQGETSKITVWVKPLKEGCCFTAATVCACPEIRSVTKCGQPAICVKQEGPECACLRCPVTYKIHVINQGTATARNVVLENPVPDGFAHTSGQRVLTYTLGDMQPGEQKVITVEFCPLKRGRATNIATVSYCGGHKNTASVTTVINEPCVQVNIAGADWSYVCKPVEYVISVSNPGDLILRDVVVEDTLSPGVTVIEAPGAQISCNKVVWTVKELNPGESLQYKVLVRAQTPGQFTNNVVVKSCSDCGTCTSCAEATTYWKGVAATHMCVVDTCDPVCVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSFSGPTKGTITGNTVVFDALPRLGSKETVEFSVTLKAVSAGDARGEAILSSDTLTVPVSDTENTHIY"
#> [19] "MNKLIRRAVTIFAVTSVASLFASGVLETSMAESLSTNVISLADTKAKNTASHHKDKKARKNHQKETPVVHNQAVAPVRESKSTGPKQDSCFGKMYTVKVNDDRNVEITQSVPEYATVGSPYPIEITAKGKRDCVDVIITQQLPCEAEFVSSDPATTPTADGKLVWKIDRLGQGEESKITVWVKPLKEGCCFTAATVCACPEIRSVTKCGQPAICVKQEGPECACLRCPVTYKIHVVNQGTATARNVVLENPVPDGFAHSSGQRVLTYTLGDMQPGEQKVVTVEFCPLKRGRATNIATVSYCGGHKNTASVTTVINEPCVQVNIAGADWSYVCKPVEYVISVSNPGDLILRDVVVEDTLSPGVTVIEAPGAQISCNKVVWTVKELNPGESLQYKVLVRAQTPGQFTNNVVVKSCSDCGTCTSCAEATTYWKGVAATHMCVVDTCDPVCVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSFSGPTKGTITGNTVVFDALPRLGSKETVEFSVTLKAVSAGDARGEAILSSDTLTVPVSDTENTHIY"
#> [20] "MSKLIRRVVAILALTSMASSFASGKIEAAAESLSTQVVANADVVKNTAKKVRLDRKQRSQNKRDKAGSFCDGEFYPCEGNRCQTPVDTKQESCYGKMYSTRVNDDCNVEISQSVPEYATVGSPYPIEIFAVGKKDCVNVVITQQLPCEVEFISSDPVSTPTADGKLIWTIDRLGQGEKCKITVWVKPLKEGCCFTAATVCACPELRSYTKCGQPAICIKQEGPECACLRCPVCYKIEVCNTGSAIARNVVVDNPVPDGFYHSSGQRVLSFNLGDMRPGESKVFTVEFCPQKRGRITNVATVSYCGGHKCSANVTTIVNEPCVQVNISGADWSYVCKPVEYMISVSNPGDLKLYDVVIEDLLPSGITILEAAGAEICCNKAVWCIKEICPGETLQFKVVVKAQNPGKFTNQVSVKTQSDCGSCTSCADITTHWKGLAATHMCVIDTNDPICVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSSSGPTKGTITGNTVVFDALPKLGSKESVEFSVTLKGIAPGDARGEAILSSDTLTVPVTDVENTHVY"
#> [21] "MSKLIRRVVTVLALTSMTSSFASGGIEAAVAESLMTKIIANAESKPAADHKKEAKHNRNKKHSKATKHNSRSNPSCCDKEFFPCEEKNCQQVESRQESCFGKMYSIKVNDDCNVELSQSVPEYATVGSPYPIEILAIGKKDCVNVVITQQLPCEAEFVSSDPETTPTADGKLMWKIDRLGQGERCKITVWVKPIKEGCCFTAATVCACPEIRSYTKCGQPAICIKQEGPDCACLRCPVRYKIEVSNTGSAIARNVVVDNPVPDGFSHASGQRVLSFNLGDMHPGESKVLCVEFCPQKRGQVTNVATVSYCGGHKCSANVMTVINEPCVNVTISGVDWAYVCKPVEYTITVSNPGDLVLRNVVVEDNLPGSALILEAAGAEISCNKAVWCIKELCPGETLQFKVLVKAQVTG"
#> [22] "MSKLIRRVVTALALTSMASCFASGGIEAAVAESLITKIIANAGTSTTPVTAKKVKVVRKNKLEQNSFCDREFYPCEEGRNQSVEAQQESCYGKLYSVKVNDDNNVEICQSVPEYATVGSPYPIEILAIGKRDCVDVMITQQLPCEAEFVSSDPITTPTSDGRLIWKIDRLGYGEKCKITVWVKPLKEGCCFTAATVCACPELRSYTKCGQPAICIKQDGPECACLKCPVCYKIEVVNTGSAVARNVSVENPVPDGYSHATGQRVLSFNLGDMKPGEKKVFTLEFCPQKRGQVTNIATVTYCGGHKCAASVTTVINESCVQVNITGSDWSYVCKPVEYSISVSNPGDLVLTDVMIEDVTPIGASVLEAPGAEICCNKVVWRIKEMCPGETLQFKVVLKAQAPGRFTNQVMVKTNSDCGTCTSCAEATTHWKGLAAIHMCVLDTNDPICVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPLASSGPTKGTISGNTVVFDALPKLGSKESVEFSVTLKGIAPGDARGEAILSSDTLTSPVSDTENTHIY"
#> [23] "MTKLIRRVVTVLALTSMTSSFASGGIEAAVAESLMTKIIANAESKPAADHKKEAKHNRNKKHSKATKHNSRSNPSCCDKEFFPCEEKNCQQVESRQESCFGKMYSIKVNDDCNVELSQSVPEYATVGSPYPIEILAIGKKDCVNVVITQQLPCEAEFVSSDPETTPTADGKLMWKIDRLGQGERCKITVWVKPIKEGCCFTAATVCACPEIRSYTKCGQPAICIKQEGPDCACLRCPVRYKIEVSNTGSAIARNVVVDNPVPDGFSHASGQRVLSFNLGDMHPGESKVLCVEFCPQKRGQVTNVATVSYCGGHKCSANVMTVINEPCVNVTISGVDWAYVCKPVEYTITVSNPGDLVLRNVVVEDNLPGSALILEAAGAEISCNKAVWCIKELCPGETLQFKVLVKAQVPGQITSQVVVNSQSDCGACTSCADATTYWKGLAATHMCVIDTNDPICVGENTVYRICITNRGSAEDTNVSLILKFSKELQPISSSGPTKGTISGNTVIFDALPKLGSKESVEFSVTLKGVAPGDARGEAVLSSDTLTSPVSDVENTHVY"
#> [24] "MSKLIRRVVTVLALTSMASSFASGKIEAAAAESLATRFIASTENSDDNVFQATAKKVRFGRNKNQRQEQKHTGAFCDKEFYPCEGGQCQPVEATQESCYGKMYCVRVNDDCNVEISQSVPEYATVGSPYPIEILALGKKDCVNVVITQQLPCEVEFVSSDPATTPTSDSKLIWTIDRLGQGEKCKITVWVKPLKEGCCFTAATVCACPELRSYTKCGQPAICIKQEGPECACLRCPVCYKIEVCNTGSAIARNVVVDNPVPDGYTHASGQRVLSFNLGDMRPGDSKCFCVEFCPQKRGKVTNVATVSYCGGHKCSANVTTVVNEPCVQVNISGADWSYVCKPVEYTIVVSNPGDLKLYDVVIEDTAPSGATILEAAGAEICCNKAVWCIKEMCPGETLQFKVVAKAQSPGKFTNQVVVKTNSDCGTCTSCAEVTTHWKGLAATHMCVIDTNDPICVGENTVYRICVTNRGSAEDTNVSLILKFSKELQPVSSSGPTKGTITGNTVVFDALPKLGSKESVEFSVTLKGIAPGDARGEAILSSDTLTVPVADTENTHVY"
...
defline <- cpafx$xmlValue("//TSeq_defline")
defline
#> [1] "outer membrane complex protein OmcB [Chlamydia abortus]"
#> [2] "outer membrane complex protein OmcB [Chlamydia abortus]"
#> [3] "outer membrane complex protein OmcB [Chlamydia abortus]"
#> [4] "outer membrane complex protein OmcB [Chlamydia buteonis]"
#> [5] "outer membrane complex protein OmcB [Chlamydia sp. S15-834C]"
#> [6] "outer membrane complex protein OmcB [Chlamydia suis]"
#> [7] "outer membrane complex protein OmcB [Chlamydia sp. H15-1957-10C]"
#> [8] "outer membrane complex protein OmcB [Candidatus Chlamydia corallus]"
#> [9] "outer membrane complex protein OmcB [Chlamydia suis]"
#> [10] "outer membrane complex protein OmcB [Chlamydia suis]"
#> [11] "outer membrane complex protein OmcB [Chlamydia abortus]"
#> [12] "outer membrane complex protein OmcB [Chlamydia suis]"
#> [13] "outer membrane complex protein OmcB [Chlamydia suis]"
#> [14] "outer membrane complex protein OmcB [Chlamydia suis]"
#> [15] "outer membrane complex protein OmcB [Chlamydia abortus]"
#> [16] "outer membrane complex protein OmcB [Chlamydia suis]"
#> [17] "outer membrane complex protein OmcB [Chlamydia suis]"
#> [18] "outer membrane complex protein OmcB [Chlamydia suis]"
#> [19] "outer membrane complex protein OmcB [Chlamydia suis]"
#> [20] "outer membrane complex protein OmcB [Chlamydia gallinacea]"
#> [21] "outer membrane complex protein OmcB, partial [Chlamydia psittaci]"
#> [22] "outer membrane complex protein OmcB [Chlamydia sp. 2742-308]"
#> [23] "outer membrane complex protein OmcB [Chlamydia pecorum]"
#> [24] "outer membrane complex protein OmcB [Chlamydia psittaci]"
...einfo: Information about the Entrez databases
You can use einfo to obtain a list of all database names accessible
through the Entrez utilities:
einfo()
#> Object of class 'einfo'
#> List of Entrez databases
#> [1] "pubmed" "protein" "nuccore" "ipg"
#> [5] "nucleotide" "structure" "sparcle" "genome"
#> [9] "annotinfo" "assembly" "bioproject" "biosample"
#> [13] "blastdbinfo" "books" "cdd" "clinvar"
#> [17] "gap" "gapplus" "grasp" "dbvar"
#> [21] "gene" "gds" "geoprofiles" "homologene"
#> [25] "medgen" "mesh" "ncbisearch" "nlmcatalog"
#> [29] "omim" "orgtrack" "pmc" "popset"
#> [33] "proteinclusters" "pcassay" "biosystems" "pccompound"
#> [37] "pcsubstance" "seqannot" "snp" "sra"
#> [41] "taxonomy" "biocollections" "gtr"For each of these databases, we can use einfo again to obtain more
information:
einfo("taxonomy")
#> Object of class 'einfo'
#> Overview over the Entrez database 'Taxonomy'.
#> dbName: taxonomy
#> MenuName: Taxonomy
#> Description: Taxonomy db
#> DbBuild: Build201008-0820.1
#> Count: 2408023
#> LastUpdate: 2020-10-08 09:46:00
#> Fields: Name; FullName; Description; TermCount; IsDate; IsNumerical; Single...
#> Links: Name; Menu; Description; DbTo