medic 2.4.1

A command line tool to manage a PubMed DB mirror.

The Swiss Army knife to parse MEDLINE XML files or download eUtils’ PubMed XML records, bootstrapping a local MEDLINE/PubMed database, updating and/or deleting the records, and writing the contents of selected PMIDs into flat-files. A more in-depth tutorial for this tool is part of my blog.

DOI:10.5281/zendo.9968

Synopsis

medic [options] CMD FILE|PMID...

man medic
medic --help
medic --output /tmp parse baseline/medline*.xml.gz
medic --update parse update/medline*.xml.gz
medic --info delete delete.txt
medic --url sqlite:///tmp.db insert pubmed.xml
medic --pmid-lists update pmids_to_fetch_online.txt
medic --all update medline13n1000.xml
medic --format html write 1028734 1298474 > out.html
medic --logfile log.txt write pmid_list.txt

Setup

If you are not using pip install medic, install all dependencies/requirements:

pip install sqlalchemy
# only if using python3 < 3.2:
pip install argparse

Install the DB driver you prefer to use (supported are PostgreSQL and SQLite, with the latter part of the Python StdLib):

pip install psycopg2

Create the PostgreSQL database:

createdb medline

If you are fine working with SQLite, you only need to use the path to the SQLite DB file in the URL option (that will implicitly “create” the DB):

medic insert --url sqlite:///tmp.db 123456

To create the tables in an empty DB, you can just “try” to fetch a record: As the DB is empty, this will not write anything, but SQL Alchemy will create the tables for you in the DB:

medic write 123 # for PostgreSQL
medic --url sqlite:///tmp.db write 123 # for SQLite

Description

medic [options] COMMAND PMID|FILE...

The --url URL option represents the DSN of the database and might be needed (default: postgresql://localhost/medline); For example:

PostgreSQL

postgresql://host//dbname

SQLite DB

sqlite:////absolute/path/to/foo.db or sqlite:///relative/path/to/foo.db

The five COMMAND arguments:

insert

Create records in the DB by parsing MEDLINE XML files or by downloading PubMed XML from NCBI eUtils for a list of PMIDs. The insert fails if the record already exists in the DB.

write *

Write records as MEDLINE files to a directory, each file named as “<pmid>.txt”. Alternatively, just the TIAB (title and abstract) plain-text can be output, and finally, a single file in TSV or HTML format can be generated (see option --format). If the requested PMID does not exist in the DB, the command does not fail, but the relevant file, row, or element will not have been written.

update

Insert or update records in the DB (instead of creating them); note that if a record exists, but is added with create, this would throw an IntegrityError. If you are not sure if the records are in the DB or not, use update (N.B. that update is slower).

delete *

Delete records from the DB for a list of PMIDs (using --pmid-lists)

parse

Does not interact with the DB, but rather creates “.tab” files for each table that later can be used to load a database, particularly useful when bootstrapping a large collection.

* Note that write and delete can only use PMID lists (option --pmid-lists), so for these two commands, that option is always active (implicitly).

For example, to download two PubMed records by PMID and update them in the DB:

medic update 100000 123456

Add a single MEDLINE or PubMed XML file to the database:

medic insert pudmed.xml

Note that if the suffix “.gz” is present, the parser automatically decompresses the XML file(s) first. This feature only works with GNU-zipped files and the “.gz” suffix must be present.

Export a few records from the database as HTML (to “articles.html”):

medic write --format html --output articles.html 292837491 128374 213487

Write the content of the entire database (in MEDLINE format, to STDOUT):

medic write ALL

Therefore, command line arguments are treated as follows:

integer values

are always treated as PMIDs to download PubMed XML data

all other values

are always treated as MEDLINE XML files to parse unless you use the option --pmid-lists

files ending in “.gz”

are treated as gzipped MEDLINE XML files

Requirements

• Python 3.2+

• SQL Alchemy 0.8+

• PostgreSQL 8.4+ or SQLite 3.7+

Note that while any DB supported by SQL Alchemy should work, all other DBs are untested.

Loading MEDLINE

Please be aware that the MEDLINE distribution is not unique, meaning that it contains a few records multiple times (see the section about Version IDs).

Parsing and loading the baseline into a PostgreSQL DB on the same machine:

medic parse baseline/medline14n*.xml.gz

for table in citations abstracts authors chemicals databases \
descriptors identifiers keywords publication_types qualifiers sections;
  do psql medline -c "COPY $table FROM '`pwd`/${table}.tab';";
done

For the update files, you need to go one-by-one, adding each one in order, and using the flag --update when parsing the XML. After parsing an XML file and before loading the dump, run medic delete delete.txt to get rid of all entities that will be updated or should be removed (PMIDs listed as DeleteCitations):

# parse a MEDLINE update file:
medic --update parse medline14n1234.xml.gz

# delete its updated and DeleteCitation records:
medic delete delete.txt

# load (COPY) all tables for that MEDLINE file:
for table in citations abstracts authors chemicals databases \
descriptors identifiers keywords publication_types qualifiers sections;
  do psql medline -c "COPY $table FROM '`pwd`/${table}.tab';";
done

Alternatively - simpler but slower - you can just update from the XML directly:

medic update medline14n1234.xml.gz

Version IDs

MEDLINE has began to use versions to allow publishers to add multiple citations for the same PMID. This only occurs with 71 articles from one journal, “PLOS Curr”, in the 2013 baseline, creating a total of 149 non-unique records.

As this is the only journal and as there may only be one record per PMID in the database, alternative versions are currently being ignored. In other words, if a MedlineCitation has a VersionID value other than “1”, those records can be skipped to avoid DB errors from non-unique records.

For example, in the 2013 baseline, PMID 20029614 is present ten times in the baseline, each version at a different stage of revision. Because it is the first entry (in the order they appear in the baseline files) without a VersionID or a version of “1” that is the relevant record, medic by default filters citations with other versions than “1”. If you do want to process other versions of a citation, use the option --all.

To summarize, medic by default removes alternate citations.

Database Tables

Citation (citations)

pmid:BIGINT, status:ENUM(state), year:SMALLINT, title:TEXT, journal:VARCHAR(256), pub_date:VARCHAR(256), issue:VARCHAR(256), pagination:VARCHAR(256), created:DATE, completed:DATE, revised:DATE, modified:DATE

Abstract (abstracts)

pmid:FK(Citation), source:ENUM(type), copyright:TEXT

Section (sections)

pmid:FK(Citation), source:ENUM(type), seq:SMALLINT, name:ENUM(section), label:VARCHAR(256), content:TEXT, truncated:BOOLEAN

Author (authors)

pmid:FK(Citation), pos:SMALLINT, name:TEXT, initials:VARCHAR(128), forename:VARCHAR(128), suffix:VARCHAR(128),

PublicationType (publication_types)

pmid:FK(Citation), value:VARCHAR(256)

Descriptor (descriptors)

pmid:FK(Citation), num:SMALLINT, major:BOOL, name:TEXT

Qualifier (qualifiers)

pmid:FK(Descriptor), num:FK(Descriptor), sub:SMALLINT, major:BOOL, name:TEXT

Identifier (identifiers)

pmid:FK(Citation), namespace:VARCHAR(32), value:VARCHAR(256)

Database (databases)

pmid:FK(Citation), name:VARCHAR(32), accession:VARCHAR(256)

Chemical (chemicals)

pmid:FK(Citation), idx:VARCHAR(32), uid:VARCHAR(256), name:VARCHAR(256)

Keyword (keywords)

pmid:FK(Citation), owner:ENUM(owner), cnt:SMALLINT, major:BOOL, value:TEXT

• bold (Composite) Primary Key

• italic NOT NULL (Strings that may not be NULL are also never empty.)

Supported XML Elements

Entities

• MedlineCitation and ArticleTitle (Citation and Identifier)

• Abstract and OtherAbstract (Abstract and Section)

• Author (Author)

• Chemical (Chemical)

• DataBank (Database)

• Keyword (Keyword)

• MeshHeading (Descriptor and Qualifier)

• PublicationType (PublicationType)

• DeleteCitation (for deleting records when parsing updates)

Fields/Values

• Abstract (with “NLM” as Abstract.source)

• AbstractText (Section.name “Abstract” or the NlmCategory, Section.content with Label as Section.label)

• AccessionNumber (Database.accession)

• ArticleId (Identifier.value with IdType as Identifier.namesapce; only available in online PubMed XML)

• ArticleTitle (Citation.title; if empty, use the VernacularTitle or set to “UNKNOWN”)

• CollectiveName (Author.name)

• CopyrightInformation (Abstract.copyright)

• DataBankName (Database.name)

• DateCompleted (Citation.completed)

• DateCreated (Citation.created)

• DateRevised (Citation.revised)

• DescriptorName (Descriptor.name with MajorTopicYN as Descriptor.major)

• ELocationID (Identifier.value with EIdType as Identifier.namespace)

• ForeName (Author.forename)

• Initials (Author.initials)

• Issue (Citation.issue)

• Keyword (Keyword.value with Owner as Keyword.owner and MajorTopicYN as Keyword.major)

• LastName (Author.name)

• MedlineCitation (with Status as Citation.status)

• MedlineTA (Citation.journal)

• NameOfSubstance (Chemical.name)

• MedlinePgn (Citation.pagination)

• OtherAbstract (with Type as Abstract.source)

• OtherID (Identifier.value iff Source is “PMC” with Identifier.namespace as “pmc”)

• PMID (Citation.pmid)

• PubDate (Citation.pub_date and Citation.year)

• PublicationType (PublicationType.value)

• QualifierName (Qualifier.name with MajorTopicYN as Qualifier.major)

• RegistryNumber (Chemical.uid)

• Suffix (Author.suffix)

• VernacularTitle (Citation.title if AbstractTitle is empty)

• Volume (Citation.issue)

Version History

2.4.1

• Fixed a bug while parsing “PubDate” records that asserted the wrong length. Thanks to Josef Steiner for reporting it.

2.4.0

• Added a year column to table citations to make it easier to select for the year of publication. To migrate/update your DB, run these two commands:

  ALTER TABLE citations ADD "year" smallint NOT NULL DEFAULT 0;
  UPDATE citations SET year = substring(pub_date FROM '^[12][890][0-9][0-9]')::int;

  Note that the (currently) oldest publications in MEDLINE are from 1809, from the first issue of the journal “Med Chir Trans”.

2.3.1

• Fixed a bug when fetching all records on PubMed from database with “ALL”.

2.3.0

• Added special argument “ALL” to write/delete all records.

2.2.0

• Ensured compatibility with the MEDLINE DTD updates for 2015 and cleaned some code pieces. Includes a fix for the bad (long) keyword in PMID 25114415 (with a carriage return).

• A column was added to the ORM, resulting in backwards incompatible change: From this version on, the trailing string “(ABSTRACT TRUNCATED AT xxx WORDS)” is stripped from AbstractText and instead the flag truncated has be added to table sections and is set if the string was present (but has been removed); To migrate your Postgres database, please run:

  ALTER TABLE sections ADD "truncated" boolean NOT NULL DEFAULT 'false';

  Note that for one case this produces a Section with just one whitespace character, because the original content was only the “ABSTRACT TRUNCATED…” message.

• MEDLINE formatted output is now written to STDOUT or a single file, because it makes selecting specific fields with grep very easy. Records are separated with an empty line.

2.1.7

• Work-around for the limit of SQLite that only lets you use 999 variables per query.

• Corrected the outdated VernacularTitle documentation in this document.

2.1.6

• Work-around for parsing citations that have an empty ArticleTitle element (which they shouldn’t, according to the DTD): Either use the VernacularTitle (e.g., PMID 22536004), or otherwise set the title to “UNKNOWN” (the empty string is not a valid title) and log a warning.

• Work-around for non-unique PublicationType entries (e.g., PMID 10500000): drop non-unique PublicationTypes (with the same PMID and value).

• Corrected left-over “Medline” entity names in this document to “Citation”.

2.1.5

• Added page_size=MAX and synchronous=OFF pragmas for SQLite DBs (hat-tip to Jason)

2.1.4

• A MEDLINE issue found by Jason: PMID 24073073 has an empty keyword and keyword list that should not be there; Medic prevents adding improper data to the DB by raising an AssertionError. To deal with such cases, medic now ensures each keyword is non-empty before attempting to generate a database entry and drops empty (i.e., whitespace-only) keyword data.

2.1.3

• Jason Hennessey changed the (absolute) path of medic’s man-page, set to /usr/local/share/man in the setup script, to a relative location (share/man) to avoid issues when installing medic in a virtualenv

2.1.2

• fixed a bug where SQLite did not find the implicit FK->PK reference (thanks to Jason Hennessey for reporting the issue)

2.1.1

• added SQLite temporary DB example URL to help output

• refactored HTML output code

2.1.0

• DB schema change from: records() -> sections(content) to: citations(title) -> abstracts(copyright) -> sections(content)

• name change: the entity/table Medline/records is now called Citation/citations

• title and copyright text is no longer stored in Section/sections

• added a new Abstract/abstracts entity/table with a copyright attribute (formerly stored in sections.content with name = ‘Copyright’)

• added a new citations.title attribute (formerly stored in sections.content with name = ‘Title’)

• added a new source primary-key attribute to Section and Abstract (set to either ‘NLM’ for regular Abstract elements or to the value of the OtherAbstract Type attribute for other abstracts)

• skipping “Abstract available from the publisher.”-only abstracts

2.0.2

• made the use of --pmid-lists for delete and write implicit

• added instructions to bootstrap the tables in a PostgreSQL DB

• minor improvements to this manual

• fixed a bug when inserting/updating from MEDLINE XML files

2.0.1

• fixed a bug that lead to skipping of abstracts (thanks to Chris Roeder for detecting the issue)

2.0.0

• added Keywords and PublicationTypes

• added MEDLINE publication date, volume, issue, and pagination support

• added MEDLINE output format and made it the default

• DB structure change: descriptors.major and qualifiers.major columns swapped

• DB structure change: section.name is now an untyped varchar (OtherAbstract separation)

• cleaned up the ORM test cases

1.1.1

• code cleanup (PEP8, PyFlake)

• fixed an issue where the parser would not leave the skipping state

1.1.0

• --update parse now writes a file to use with --pmid-lists delete

• fixed a bug with CRUD manager

• added a man page

1.0.2

• fixes to make the PyPi version and pip install medic work

1.0.1

• updates to the setup.py and README.rst files

1.0.0

• initial release

Copyright and License

License: GNU GPL v3. Copyright 2012-2014 Florian Leitner. All rights reserved.