Extract mutations/variants from Pubmed/PMC articles

Question

[dasilvauirajan]

How can I extract mutations/variants from Pubmed/PMC articles using terms and without need to download these articles? Any command line tool I can do that?

[GenoMax]

using terms

Which terms?

[dasilvauirajan]

For exemple, i want to extract all mutations already described for HRSV, in this case the "term" could be "HRSV"

[GenoMax]

See example below.

[dasilvauirajan]

Thanks genomax and Pierre Lindenbaum both ways are exacly what I was looking for

Answer 1

[GenoMax]

Using EntrezDirect:

$ esearch -db pubmed -query "osteoporosis" | elink -target snp | esummary | xtract -pattern DocumentSummary -element SNP_ID,NAME,SNP_CLASS,CHRPOS, DOCSUM | head -2
1085307068      GORAB   delins  1:170539555     HGVS=NC_000001.11:g.170539556_170539557del,NC_000001.10:g.170508697_170508698del,NG_012237.1:g.12435_12436del,NM_152281.2:c.483_484del,NM_001320252.1:c.-58_-57del,NM_001320252.2:c.-58_-57del,NR_027397.1:n.510_511del,NR_027397.2:n.466_467del,NM_001146039.1:c.483_484del,XM_006711628.4:c.-62_-61del,XM_011510150.3:c.-62_-61del,XM_011510149.2:c.432_433del,XM_017002807.1:c.-62_-61del,XM_024450864.1:c.-58_-57del,XM_011510151.1:c.-62_-61del,NP_689494.2:p.Lys162fs,NP_001139511.1:p.Lys162fs,XP_011508451.1:p.Lys145fs|SEQ=[GA/-]|GENE=GORAB:92344
886042603       COL1A1  del     17:50188957     HGVS=NC_000017.11:g.50188957del,NC_000017.10:g.48266318del,NG_007400.1:g.17683del,NM_000088.3:c.2991del,XM_005257058.4:c.2721del,XM_005257058.1:c.2721del,XM_005257059.4:c.2073del,XM_005257059.1:c.2073del,XM_011524341.1:c.2793del,NP_000079.2:p.Gly998fs,XP_005257115.2:p.Gly908fs,XP_005257116.2:p.Gly692fs,XP_011522643.1:p.Gly932fs|SEQ=[A/-]|GENE=COL1A1:1277

Example based on requested term:

$ esearch -db pubmed -query "HRSV" | elink -target snp | esummary | xtract -pattern DocumentSummary -element SNP_ID,NAME,SNP_CLASS,CHRPOS, DOCSUM | head -3
386834236       GAA     snv     17:80104542     HGVS=NC_000017.11:g.80104542T>G,NC_000017.10:g.78078341T>G,NG_009822.1:g.7987T>G|SEQ=[T/G]|GENE=GAA:2548
386834235       GAA     del     17:80105111     HGVS=NC_000017.11:g.80105111del,NC_000017.10:g.78078910del,NG_009822.1:g.8556del,NM_000152.5:c.525del,NM_000152.4:c.525del,NM_000152.3:c.525del,NM_001079803.3:c.525del,NM_001079803.2:c.525del,NM_001079803.1:c.525del,NM_001079804.3:c.525del,NM_001079804.2:c.525del,NM_001079804.1:c.525del,XM_005257194.4:c.525del,XM_005257194.1:c.525del,XM_005257193.2:c.525del,XM_005257193.1:c.525del,NP_000143.2:p.Glu176fs,NP_001073271.1:p.Glu176fs,NP_001073272.1:p.Glu176fs,XP_005257251.1:p.Glu176fs,XP_005257250.1:p.Glu176fs|SEQ=[T/-]|GENE=GAA:2548
121907943       GAA     snv     17:80118271     HGVS=NC_000017.11:g.80118271C>T,NC_000017.10:g.78092070C>T,NG_009822.1:g.21716C>T,NM_000152.5:c.2560C>T,NM_000152.4:c.2560C>T,NM_000152.3:c.2560C>T,NM_001079803.3:c.2560C>T,NM_001079803.2:c.2560C>T,NM_001079803.1:c.2560C>T,NM_001079804.3:c.2560C>T,NM_001079804.2:c.2560C>T,NM_001079804.1:c.2560C>T,XM_005257194.4:c.2560C>T,XM_005257194.1:c.2560C>T,XM_005257193.2:c.2560C>T,XM_005257193.1:c.2560C>T,NP_000143.2:p.Arg854Ter,NP_001073271.1:p.Arg854Ter,NP_001073272.1:p.Arg854Ter,XP_005257251.1:p.Arg854Ter,XP_005257250.1:p.Arg854Ter|SEQ=[C/T]|GENE=GAA:2548

Answer 2

[Pierre Lindenbaum]

NCBI Elink from a pubmed id (e.g: 21378989 ) maps to a dbsnp id (eg. rs387906747 ) .

wget -q -O - "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=snp&id=21378989" 


https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20101123/elink.dtd">
<eLinkResult>
  <LinkSet>
    <DbFrom>pubmed</DbFrom>
    <IdList>
      <Id>21378989</Id>
    </IdList>
    <LinkSetDb>
      <DbTo>snp</DbTo>
      <LinkName>pubmed_snp</LinkName>
      <Link>
        <Id>387906747</Id>
      </Link>
    </LinkSetDb>
  </LinkSet>
</eLinkResult>