use Entrez Direct to access NCBI database

I was reading Applied Bioinformatics 2014 lecture 3 and learned that one can use Entrez Direct to access NCBI database (Pubmed, nucleotide, protein sequence etc).

After installing Entrez Direct, I played around with it:

View this gist on GitHub

Commonly-used fields for PubMed queries include:

  [AFFL]  Affiliation       [FILT]  Filter              [MESH]  MeSH Terms
  [ALL]   All Fields        [JOUR]  Journal             [PTYP]  Publication Type
  [AUTH]  Author            [LANG]  Language            [WORD]  Text Word
  [FAUT]  Author - First    [MAJR]  MeSH Major Topic    [TITL]  Title
  [LAUT]  Author - Last     [SUBH]  MeSH Subheading     [TIAB]  Title/Abstract

[PDAT] Date - Publication [UID] UID

Filters that limit search results to subsets of PubMed include:

  humans [MESH]                has abstract [FILT]
  pharmacokinetics [MESH]      historical article [FILT]
  chemically induced [SUBH]    loprovflybase [FILT]
  all child [FILT]             randomized controlled trial [FILT]
  english [FILT]               clinical trial, phase ii [PTYP]
  free full text [FILT]        review [PTYP]

Sequence databases are indexed with a different set of search fields, including:

  [ACCN]  Accession       [GENE]  Gene Name            [PROT]  Protein Name
  [ALL]   All Fields      [JOUR]  Journal              [SQID]  SeqID String
  [AUTH]  Author          [KYWD]  Keyword              [SLEN]  Sequence Length
  [GPRJ]  BioProject      [MLWT]  Molecular Weight     [SUBS]  Substance Name
  [ECNO]  EC/RN Number    [ORGN]  Organism             [WORD]  Text Word
  [FKEY]  Feature Key     [PACC]  Primary Accession    [TITL]  Title
  [FILT]  Filter          [PROP]  Properties           [UID]   UID

and a sample query in the protein database is:

  "alcohol dehydrogenase [PROT] NOT (bacteria [ORGN] OR fungi [ORGN])"

Please refer to the documents for more examples http://www.ncbi.nlm.nih.gov/books/NBK179288/