pubmed-lookup 0.2.1

• Installation
• Usage
• Command-Line Tools
  • pubmed-citation
  • pubmed-url
• Revision History

Installation

pypi

pip install pubmed-lookup

github（开发分支）

pip install git+http://github.com/mfcovington/pubmed-lookup.git@develop

Usage

• 检索PubMed记录：

  frompubmed_lookupimportPubMedLookup# NCBI will contact user by email if excessive queries are detectedemail=''url='http://www.ncbi.nlm.nih.gov/pubmed/22331878'lookup=PubMedLookup(url,email)

• 创建发布对象：

  frompubmed_lookupimportPublicationpublication=Publication(lookup)# Use 'resolve_doi=False' to keep DOI URL

• 访问发布对象的属性：

  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),}))

• 示例输出：

  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

Revision History

0.2.1 2016年1月22日

• 更改导致travis ci失败的pubmed_lookup.command_line的导入

0.2.0 2016-01-22

• 创建命令行工具（pubmed-citation）以快速检索pubmed id/url的引用
• 创建命令行工具（pubmed-url）以快速检索pubmed id/url的文章和doi url
• 通过不解析doi url（Publication(pubmed_record, resolve_doi=False)）来添加节省时间的选项
• 清理文档

0.1.5 2016-01-08

• 为没有月份信息的发布添加异常（感谢sasha cuerda！）

0.1.4 2015年12月24日

• 解决PEP8错误
• 重构代码使其更干净
• 配置横向配置并添加代码运行状况徽章
• 将github安装说明转换为从development branch安装

0.1.3 2015年7月29日

• 添加发布和pubmedlookup的测试
• 配置Travis CI
• 配置工作服
• 在自述文件中添加pypi、travis ci和工作服徽章

0.1.2 2015年6月24日

• 准备通过PYPI分发

0.1.1 2015年5月26日

• 返回带有cite_mini（）的出版物的缩写引文
• 将安装文档更改为使用github链接，因为pypi上还没有

0.1.0 2015年5月22日

• 查找PubMed记录并使用有关科学出版物的信息创建出版物对象