Processing Flags

  -strict     Remove HTML and MathML tags
  -mixed      Allow mixed content XML

Data Source

  -input      Read XML from file instead of stdin

Local Record Cache

  -archive    Base path for saving individual XML files, plus paths
                for first- and second-level inverted index caches
  -delete     Same paths as -archive, for deleting inverted caches
  -index      Use [parent/element@attribute^version] for identifier

  -fetch      Base path for retrieving XML files
  -stream     Path for retrieving compressed XML

  -flag       [strict|mixed|none]
  -gzip       Use compression for local XML files
  -hash       Print UIDs and checksum values to stdout

  -trie       Print archive, indices, increment, or postings file path
  -padz       Pad PMIDs with leading zeros to 8 characters

Local Record Index

  -e2index    Create Entrez index XML
  -e2invert   Generate inverted index
  -join       Collect subsets of inverted index files
  -fuse       Combine subsets of inverted index files
  -merge      Combine inverted indices, divide by term prefix
  -promote    Create term lists and posting files

  -path       Path to postings directory

  -query      Search on words or phrases in Boolean formulas
  -exact      Strict search for article round-tripping
  -title      Exact search limited to indexed title field

  -count      Print terms and counts, merging wildcards
  -counts     Expand wildcards, print individual term counts

Documentation

  -help       Print this document
  -version    Print version number

Sample File Download

  nquire -dwn ftp.ncbi.nlm.nih.gov /entrez/entrezdirect/samples carotene.xml.zip
  unzip carotene.xml.zip
  rm carotene.xml.zip

Mammalian Sequence Download

  download-sequence gbmam gbpri gbrod

Human Subset Extraction

  #!/bin/sh

  for fl in gbpri?.aso.gz gbpri??.aso.gz
  do
    run-ncbi-converter asn2all -i "$fl" -a t -b -c -O 9606 -f s > ${fl%.aso.gz}.xml
  done

Populate PubMed Archive and Positional Term Index

  export EDIRECT_PUBMED_MASTER=/Volumes/cachet
  export EDIRECT_PUBMED_WORKING=/Volumes/scratch

  archive-pubmed

  index-pubmed

Retrieve from PubMed Archive

  cat subset.uid | fetch-pubmed > subset.xml

Entrez Indexing

  cat carotene.xml | rchive -strict -e2index > carotene.e2x

Index Inversion

  cat carotene.e2x | rchive -invert > carotene.inv

Merge Indices

  rchive -merge "$MASTER/Merged" carotene.inv

Create Postings

  rchive -promote "$MASTER/Postings" TIAB carotene.mrg

Record Counts

  phrase-search -count "catabolite repress*"

Wildcard Expansion

  phrase-search -counts "catabolite repress*"

Query Processing

  phrase-search -query "(literacy AND numeracy) NOT (adolescent OR child)"

  phrase-search -query "vitamin c + + common cold"

  phrase-search -query "vitamin c ~ ~ common cold"

  phrase-search -title "Genetic Control of Biochemical Reactions in Neurospora."

Citation Match Preparation

  for fl in *.seq
  do
    base=${fl%.seq}
    echo "$base" >&2
    cat "$fl" |
    gbf2ref |
    transmute -pattern "CITATION" -format compact |
    grep '<CITATION>' > "$base.xml"
  done

Citation Match Filtering

  cat *.xml |
  xtract -pattern CITATION -select STAT -equals inpress > inpress.xml

  cat *.xml |
  xtract -pattern CITATION -select STAT -equals unpub > unpub.xml

Citation Match Processing

  cat inpress.xml | ref2pmid > frominpress.xml

  cat unpub.xml | ref2pmid > fromunpub.xml

Citation Match Candidates

  cat *.xml |
  xtract -pattern CITATION -histogram STAT |
  align-columns -a rl

Large-Scale Record Retrieval

  esearch -db pubmed -query "DNA Repair [MESH]" |
  efetch -format uid |
  fetch-pubmed |
  xtract -pattern PubmedArticle -num Author |
  sort-uniq-count -n |
  reorder-columns 2 1 |
  head -n 25 |
  tee /dev/tty |
  xy-plot auth.png

XML Data Transformation

  seconds_start=$(date "+%s")
  esearch -db pubmed -query "PNAS [JOUR]" -pub abstract |
  efetch -format uid | stream-pubmed | gunzip -c |
  xtract -stops -wrp Set,Rec -pattern PubmedArticle \
    -wrp "Year" -year "PubDate/*" \
    -wrp "Abst" -words Abstract/AbstractText |
  xtract -wrp Set,Pub -pattern Rec \
    -wrp "Year" -element Year \
    -wrp "Num" -num Abst > countsByYear.xml
  for yr in {1960..2020}
  do
    cat countsByYear.xml |
    xtract -wrp Raw -pattern Pub -select Year -eq "$yr" |
    xtract -pattern Raw -lbl "$yr" -avg Num
  done |
  tee /dev/tty |
  xy-plot verbosity.png
  rm countsByYear.xml
  seconds_end=$(date "+%s")
  seconds=$((seconds_end - seconds_start))
  echo "$seconds seconds"

Annotation Timeline

  cat $EDIRECT_PUBMED_MASTER/Current/*.xml |
  xtract -wrp Set,Rec -pattern PubmedArticle \
    -if PubDate/Month -wrp YR -year "PubDate/*" -wrp MN -len PubDate/Month |
  xtract -wrp Set,Rec -pattern Rec \
    -pfx "
" -sep "+-" -sfx "-
" -element YR,MN |
  xtract -pattern Rec -histogram DT |
  reorder-columns 2 1 | tr '+' '\t' |
  sed -e 's/-3-/1/g' -e 's/-2-/2/g' -e 's/-1-/3/g' -e 's/-[0-9]-/4/g' |
  sort -k 1,1n -k 2,2n > rawMonthCounts.txt

  result=$( cat rawMonthCounts.txt | cut -f 1 | uniq )
  for i in {1..4}
  do
    current=$( cat rawMonthCounts.txt | grep "\t$i\t" | cut -f 1,3 )
    result=$(join -a 1 -t $'\t' <(echo "$result") <(echo "$current"))
  done
  echo "$result" > plotme.txt

Query Automation

  ascend_mesh_tree() {
    var="${1%\*}"
    target=""
    ev=$( rchive -local pubmed )
    if [ -n "$ev" ]
    then
      # only care about master volume and its Data subfolder
      target="${ev%:*}"
      target=${target%/}
    fi
    while :
    do
      frst=$( phrase-search -count "$var* [TREE]" )
      scnd=$( cat "${target}/Data/meshconv.xml" |
              xtract -pattern Rec -if Tree -equals "$var" -first Code Name )
      printf "${frst}\t${scnd}\n"
      case "$var" in
        *.* ) var="${var%????}" ;;
        *   ) break             ;;
      esac
    done |
    align-columns -g 4
  }

  ascend_mesh_tree "C14.907.617.812"

  6584       c14 907 617 812*
  50722      c14 907 617*
  1567114    c14 907*
  2232414    c14*

Medical Subject Heading Code Viewer

  https://meshb.nlm.nih.gov/treeView

DISABLE ANTI-VIRUS FILE SCANNING FOR LOCAL ARCHIVES OR DESIGNATE AS TRUSTED FILES

DISABLE SPOTLIGHT INDEXING FOR EXTERNAL DISKS CONTAINING LOCAL ARCHIVES
