path: root/phrase-search

#!/bin/sh

target=""
mode="query"
field=""
debug=false

while [ $# -gt 0 ]
do
  case "$1" in
    -h | -help | --help )
      mode=help
      break
      ;;
    -debug )
      debug=true
      shift
      ;;
    -path | -master )
      target=$2
      shift
      shift
      ;;
    -count )
      mode="count"
      shift
      ;;
    -counts )
      mode="counts"
      shift
      ;;
    -countr )
      mode="countr"
      shift
      ;;
    -countp )
      mode="countp"
      shift
      ;;
    -query | -phrase )
      mode="query"
      shift
      ;;
    -filter )
      mode="filter"
      shift
      ;;
    -search )
      mode="search"
      shift
      ;;
    -exact )
      mode="exact"
      shift
      ;;
    -mock )
      mode="mock"
      shift
      ;;
    -mocks )
      mode="mocks"
      shift
      ;;
    -mockx )
      mode="mockx"
      shift
      ;;
    -term | -terms )
      mode="terms"
      shift
      if [ $# -gt 0 ]
      then
        field=$1
       shift
      fi
      ;;
    -* )
      exec >&2
      echo "$0: Unrecognized option $1"
      exit 1
      ;;
    * )
      break
      ;;
  esac
done

if [ $mode = "help" ]
then
  cat <<EOF
USAGE: $0
       [-path path_to_pubmed_master]
       -count | -counts | -query | -filter | -exact | -terms
       query arguments

EXAMPLES:

  phrase-search -terms NORM

  phrase-search -count "catabolite repress*"

  phrase-search -counts "catabolite repress*"

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

  phrase-search -query "selective serotonin reuptake inhibit*"

  phrase-search -query "monoamine oxidase inhibitor [STEM]"

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

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

  phrase-search -query "C02.782.417* [TREE] AND 2015:2018 [YEAR]"

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

AUTOMATION:

  ascend_mesh_tree() {
    var="${1%\*}"
    while :
    do
      phrase-search -count "$var* [TREE]"
      case "$var" in
        *.* ) var="${var%????}" ;;
        *   ) break             ;;
      esac
    done
  }

  ascend_mesh_tree "C14.907.617.812"

  declare -a THEMES
  THEMES=( A+ A- Bc Bg C D Ec Ec+ Ec- Eg \\
           Eg+ G H I Jc Jg K L Md Mp N O Pa \\
           Pr Q Rg Sa T Te U Ud V+ W X Y Z )
  declare -a REMAINS
  REMAINS=("${THEMES[@]:1}")

  for fst in ${THEMES[@]}
  do
    num=$(phrase-search -query "$fst [THME]" | wc -l)
    echo -e "$fst\t \t$num"
    for scd in ${REMAINS[@]}
    do
      num=$(phrase-search -query "$fst [THME] AND $scd [THME]" | wc -l)
      echo -e "$fst\t$scd\t$num"
      echo -e "$scd\t$fst\t$num"
    done
    REMAINS=("${REMAINS[@]:1}")
  done | sort | expand -t 7,13

ENTREZ INTEGRATION

  esearch -db pubmed -query "complement system proteins [MESH]" -pub clinical |
  efetch -format uid |
  phrase-search -filter "L [THME] AND D03* [TREE]"

MESH DISEASES

  C01 – bacterial infections and mycoses
  C02 – virus diseases
  C03 – parasitic diseases
  C04 – neoplasms
  C05 – musculoskeletal diseases
  C06 – digestive system diseases
  C07 – stomatognathic diseases
  C08 – respiratory tract diseases
  C09 – otorhinolaryngologic diseases
  C10 – nervous system diseases
  C11 – eye diseases
  C12 – male urogenital diseases
  C13 – female urogenital diseases and pregnancy complications
  C14 – cardiovascular diseases
  C15 – hemic and lymphatic diseases
  C16 – congenital, hereditary, and neonatal diseases and abnormalities
  C17 – skin and connective tissue diseases
  C18 – nutritional and metabolic diseases
  C19 – endocrine system diseases
  C20 – immune system diseases
  C21 – disorders of environmental origin
  C22 – animal diseases
  C23 – pathological conditions, signs and symptoms
  C24 - occupational diseases
  C25 - chemically-induced disorders
  C26 - wounds and injuries

MESH CHEMICALS AND DRUGS

  D01 – inorganic chemicals
  D02 – organic chemicals
  D03 – heterocyclic compounds
  D04 – polycyclic compounds
  D05 – macromolecular substances
  D06 – hormones, hormone substitutes, and hormone antagonists
  D08 – enzymes and coenzymes
  D09 – carbohydrates
  D10 – lipids
  D12 – amino acids, peptides, and proteins
  D13 – nucleic acids, nucleotides, and nucleosides
  D20 – complex mixtures
  D23 – biological factors
  D25 – biomedical and dental materials
  D26 – pharmaceutical preparations
  D27 – chemical actions and uses

THEME CODES:

Chemical-Gene

  A+    agonism, activation
  A-    antagonism, blocking
  Bc    binding, ligand (especially receptors)
  Ec+   increases expression/production
  Ec-   decreases expression/production
  Ec    affects expression/production (neutral)
  N     inhibits

Gene-Chemical

  O     transport, channels
  K     metabolism, pharmacokinetics
  Z     enzyme activity

Chemical-Disease

  T     treatment/therapy (including investigatory)
  C     inhibits cell growth (especially cancers)
  Sa    side effect/adverse event
  Pr    prevents, suppresses
  Pa    alleviates, reduces
  Jc    role in disease pathogenesis

Disease-Chemical

  Mp    biomarkers (of disease progression)

Gene-Disease

  U     causal mutations
  Ud    mutations affecting disease course
  D     drug targets
  Jg    role in pathogenesis
  Te    possible therapeutic effect
  Y     polymorphisms alter risk
  G     promotes progression

Disease-Gene

  Md    biomarkers (diagnostic)
  X     overexpression in disease
  L     improper regulation linked to disease

Gene-Gene

  Bg    binding, ligand (especially receptors)
  W     enhances response
  V+    activates, stimulates
  Eg+   increases expression/production
  Eg    affects expression/production (neutral)
  I     signaling pathway
  H     same protein or complex
  Rg    regulation
  Q     production by cell population

EOF
  exit
fi

if [ -z "$target" ]
then
  if [ -z "${EDIRECT_PUBMED_MASTER}" ]
  then
    echo "Must supply path to postings files or set EDIRECT_PUBMED_MASTER environment variable"
    exit 1
  else
    MASTER="${EDIRECT_PUBMED_MASTER}"
    MASTER=${MASTER%/}
    target="$MASTER/Postings"
  fi
else
  argument="$target"
  target=$(cd "$argument" && pwd)
  target=${target%/}
  case "$target" in
    */Postings ) ;;
    * ) target=$target/Postings ;;
  esac
fi

osname=`uname -s | sed -e 's/_NT-.*$/_NT/; s/^MINGW[0-9]*/CYGWIN/'`
if [ "$osname" = "CYGWIN_NT" -a -x /bin/cygpath ]
then
  target=`cygpath -w "$target"`
fi

target=${target%/}

if [ "$debug" = true ]
then
  echo "mode: $mode, path: '$target', args: '$*'"
  exit
fi

case "$mode" in
   count )
     rchive -path "$target" -count "$*" 
     ;;
   counts )
     rchive -path "$target" -counts "$*" 
     ;;
   countr )
     rchive -path "$target" -countr "$*" 
     ;;
   countp )
     rchive -path "$target" -countp "$*" 
     ;;
   query )
     rchive -path "$target" -query "$*"
     ;;
   filter )
     case "$*" in
       "AND "* | "OR "* | "NOT "* )
         rchive -path "$target" -query "[PIPE] $*"
         ;;
       "[PIPE] "* )
         rchive -path "$target" -query "$*"
         ;;
       *)
         rchive -path "$target" -query "[PIPE] AND $*"
         ;;
     esac
     ;;
   search )
     rchive -path "$target" -search "$*"
     ;;
   exact )
     rchive -path "$target" -exact "$*"
     ;;
   mock )
     rchive -path "$target" -mock "$*"
     ;;
   mocks )
     rchive -path "$target" -mocks "$*"
     ;;
   mockx )
     rchive -path "$target" -mockx "$*"
     ;;
   terms )
     if [ -z "$field" ]
     then
       cd "$target"
       for dr in *
       do
         if [ -d "$dr" ]
         then
           echo "$dr"
         fi
       done
     else
       for dr in "$target/$field"/*
       do
         if [ -d "$dr" ]
         then
           find "$dr" -name "*.$field.trm" -print0 | sort -Vz | xargs -0 cat
         fi
       done
     fi
     ;;
esac