Metadata-Version: 1.1
Name: pubmed-lookup
Version: 0.2.1
Summary: Lookup PubMed records and make Publication objects with info about a scientific publication
Home-page: https://github.com/mfcovington/pubmed-lookup
Author: Michael F. Covington
Author-email: mfcovington@gmail.com
License: BSD License
Description: *************
        pubmed-lookup
        *************
        
        
        .. image:: https://badge.fury.io/py/pubmed-lookup.svg
            :target: http://badge.fury.io/py/pubmed-lookup
            :alt: PyPI Version
        
        .. image:: https://travis-ci.org/mfcovington/pubmed-lookup.svg?branch=master
            :target: https://travis-ci.org/mfcovington/pubmed-lookup
            :alt: Build Status
        
        .. image:: https://coveralls.io/repos/mfcovington/pubmed-lookup/badge.svg?branch=master&service=github
            :target: https://coveralls.io/github/mfcovington/pubmed-lookup?branch=master
            :alt: Test Coverage
        
        .. image:: https://landscape.io/github/mfcovington/pubmed-lookup/master/landscape.svg?style=flat
           :target: https://landscape.io/github/mfcovington/pubmed-lookup/master
           :alt: Code Health
        
        ``pubmed-lookup`` is a Python package to lookup PubMed records and make Publication objects with info about a scientific publication.
        
        Source code is available on GitHub at `mfcovington/pubmed-lookup <https://github.com/mfcovington/pubmed-lookup>`_.
        
        .. contents:: :local:
        
        
        Installation
        ============
        
        **PyPI**
        
        .. code-block:: sh
        
            pip install pubmed-lookup
        
        **GitHub (development branch)**
        
        .. code-block:: sh
        
            pip install git+http://github.com/mfcovington/pubmed-lookup.git@develop
        
        
        Usage
        =====
        
        - Retrieve a PubMed record:
        
          .. code-block:: python
        
              from pubmed_lookup import PubMedLookup
        
              # NCBI will contact user by email if excessive queries are detected
              email = ''
              url = 'http://www.ncbi.nlm.nih.gov/pubmed/22331878'
              lookup = PubMedLookup(url, email)
        
        
        - Create a Publication object:
        
          .. code-block:: python
        
              from pubmed_lookup import Publication
            
              publication = Publication(lookup)    # Use 'resolve_doi=False' to keep DOI URL
        
        
        - Access the Publication object's attributes:
        
          .. code-block:: python
          
              print(
              """
              TITLE:\n{title}\n
              AUTHORS:\n{authors}\n
              JOURNAL:\n{journal}\n
              YEAR:\n{year}\n
              MONTH:\n{month}\n
              DAY:\n{day}\n
              URL:\n{url}\n
              PUBMED:\n{pubmed}\n
              CITATION:\n{citation}\n
              MINICITATION:\n{mini_citation}\n
              ABSTRACT:\n{abstract}\n
              """
              .format(**{
                  'title': publication.title,
                  'authors': publication.authors,
                  'journal': publication.journal,
                  'year': publication.year,
                  'month': publication.month,
                  'day': publication.day,
                  'url': publication.url,
                  'pubmed': publication.pubmed_url,
                  'citation': publication.cite(),
                  'mini_citation': publication.cite_mini(),
                  'abstract': repr(publication.abstract),
              }))
        
        
        - Output of example:
        
            TITLE:
            Arabidopsis synchronizes jasmonate-mediated defense with insect circadian behavior.
            
            AUTHORS:
            Goodspeed D, Chehab EW, Min-Venditti A, Braam J, Covington MF
            
            JOURNAL:
            Proc Natl Acad Sci U S A
            
            YEAR:
            2012
            
            MONTH:
            3
            
            DAY:
            20
            
            URL:
            http://www.pnas.org/content/109/12/4674
            
            PUBMED:
            http://www.ncbi.nlm.nih.gov/pubmed/22331878
            
            CITATION:
            Goodspeed D, Chehab EW, Min-Venditti A, Braam J, Covington MF (2012). Arabidopsis synchronizes jasmonate-mediated defense with insect circadian behavior. Proc Natl Acad Sci U S A 109(12): 4674-7.
            
            MINICITATION:
            Goodspeed D - Covington MF - 2012 - Proc Natl Acad Sci U S A
            
            ABSTRACT:
            Diverse life forms have evolved internal clocks enabling them to monitor time and thereby anticipate the daily environmental changes caused by Earth's rotation. The plant circadian clock regulates expression of about one-third of the Arabidopsis genome, yet the physiological relevance of this regulation is not fully understood. Here we show that the circadian clock, acting with hormone signals, provides selective advantage to plants through anticipation of and enhanced defense against herbivory. We found that cabbage loopers (Trichoplusia ni) display rhythmic feeding behavior that is sustained under constant conditions, and plants entrained in light/dark cycles coincident with the entrainment of the T. ni suffer only moderate tissue loss due to herbivory. In contrast, plants entrained out-of-phase relative to the insects are significantly more susceptible to attack. The in-phase entrainment advantage is lost in plants with arrhythmic clocks or deficient in jasmonate hormone; thus, both the circadian clock and jasmonates are required. Circadian jasmonate accumulation occurs in a phase pattern consistent with preparation for the onset of peak circadian insect feeding behavior, providing evidence for the underlying mechanism of clock-enhanced herbivory resistance. Furthermore, we find that salicylate, a hormone involved in biotrophic defense that often acts antagonistically to jasmonates, accumulates in opposite phase to jasmonates. Our results demonstrate that the plant circadian clock provides a strong physiological advantage by performing a critical role in Arabidopsis defense."
        
        
        Command-Line Tools
        ==================
        
        pubmed-citation
        ---------------
        
        - Get a PubMed record's citation (both give same result):
        
          .. code-block:: sh
        
              pubmed-citation 22331878
              pubmed-citation http://www.ncbi.nlm.nih.gov/pubmed/22331878
        
        
        - Output of example:
        
            Goodspeed D, Chehab EW, Min-Venditti A, Braam J, Covington MF (2012). Arabidopsis synchronizes jasmonate-mediated defense with insect circadian behavior. Proc Natl Acad Sci U S A 109(12): 4674-7.
        
        - Output of example (using ``--mini`` option):
        
            Goodspeed D - Covington MF - 2012 - Proc Natl Acad Sci U S A
        
        
        pubmed-url
        ----------
        
        - Get a PubMed record's url (both give same result):
        
          .. code-block:: sh
          
              pubmed-url 22331878
              pubmed-url http://www.ncbi.nlm.nih.gov/pubmed/22331878
        
        
        - Output of example:
        
            http://www.pnas.org/content/109/12/4674
        
        - Output of example (using ``--doi`` option):
        
            http://dx.doi.org/10.1073/pnas.1116368109
        
        
        *Version 0.2.1*
        
        
        Revision History
        ================
        
        0.2.1 2016-01-22
        
        - Change import of ``pubmed_lookup.command_line`` that was causing Travis CI to fail
        
        
        0.2.0 2016-01-22
        
        - Create command-line tool (``pubmed-citation``) to quickly retrieve citations for PubMed IDs/URLS
        - Create command-line tool (``pubmed-url``) to quickly retrieve article and DOI URLs for PubMed IDs/URLS
        - Add option to save time by not resolving DOI URL (``Publication(pubmed_record, resolve_doi=False)``)
        - Clean up documentation
        
        
        0.1.5 2016-01-08
        
        - Add exception for publications that do not have month information (Thanks to Sasha Cuerda!)
        
        
        0.1.4 2015-12-24
        
        - Resolve PEP8 errors
        - Refactor code to be cleaner
        - Configure Landscape and add code health badge
        - Convert Github installation instructions to install from develop branch
        
        
        0.1.3 2015-07-29
        
        - Add tests for Publication and PubMedLookup
        - Configure Travis-CI
        - Configure Coveralls
        - Add PyPI, Travis-CI, and Coveralls badges to README
        
        
        0.1.2 2015-06-24
        
        - Prepare for distribution via PyPI
        
        
        0.1.1 2015-05-26
        
        - Return an abbreviated citation for a Publication with cite_mini()
        - Change install docs to use GitHub link, since not yet on PyPI
        
        
        0.1.0 2015-05-22
        
        - Lookup PubMed records and make Publication objects with info about a scientific publication
        
        
Keywords: citations lab literature pmid publications pubmed science
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3 :: Only
