I found source code plagiarism a year ago and reported this case to BMC Systems Biology:
I listed source code of many functions that are exactly copied from GOSemSim with only function name changed in my email. The detail of source code plagiarism can also be found at Proper use of GOSemSim.
ppiPre抄袭了GOSemSim的代码，证据当然非常充分，比对一下代码就知道了，我在Proper use of GOSemSim一文中，做出了一些比较，另外也可以参考github页面，github记录了ppiPre被暴光抄袭之后所做的修改。 从我给BMC Systems Biology的编辑反馈这件事开始，在这铁板钉钉的事实面前，编辑拖了整整一年，而这一年时间过去了，ppiPre仍没有被编辑部受理。从最早反应这件事情，编辑信誓旦旦说他们很重视这种事情，到后面对我的邮件视而不见，我愿意相信编辑部处理这些事情，需要时间，他们有自己的规则，但一年的时间，不回邮件，冷处理以淡化此事，这绝对不是应该有的规则。 在编辑一直无视我的情况下，我写出了Proper use of GOSemSim一文，列举了一些一模一样的代码，并告知CRAN，当ppiPre被CRAN移除时，我写信给编辑，这时候，编辑告诉我说他们准备要去联系作者了，这时候已经过去半年了，是的！你没有看错，半年过去了，编辑说他们还没去联系作者！我是不相信的。必然是联系了之后，有某些不为人知的原因，所以编辑态度反常，对抄袭这种打鸡血的事情，不断在打太极。
再过二个月，ppiPre的作者邓岳给我写了信：
Co-IP is usually used to identified interactions among specific proteins. It is widely used in detecting protein complex. Unfortunately, an identified protein may not be an interactor, and sometimes can be a background contaminant. Ranking proteins can help us to focus a study on a few high quality candidates for subsequent interaction investigation. My R package GOSemSim has been used in many studies to investigate protein protein interaction, see 1, 2, 3, 4 and more.
GOSemSim was first implemented in 2008 and published in Bioinformatics in 2010. It’s now a mature package with no bugs found in the past half year. Only vignette and Information content data were updated.
One day, I am looking for R packages that can analyze PPI and after searching, I found the ppiPre package in CRAN.
08年的时候，结合mRNA芯片和miRNA芯片数据，做靶标预测。某一天晚上，没睡着，想到可以通过靶标来计算miRNA的相似性，正好可以利用当时写的软件包GOSemSim来计算。
09年看到BMC Systems Biology上有一篇文章，利用miRNA所调控的蛋白相互作用网络对miRNA进行聚类，当时我就觉得，利用靶标来计算，这想法不发出去，它就不再新鲜了。
记得Watson说过，科研有三大动力，其一是赶在竞争对手之前，其二用于泡妞，其三，忘记了-,-
第三点和Watson对不上，所以记不住，第一是DNA双螺旋时，谁看到那个X射线衍射结果，谁拿炸药奖，Linus Pauling当时是他们最大的竞争对手。第二点是Watson 39岁时，娶了自己的学生，19岁。
08年的时候，算好了相似性矩阵，这事就一直掠着。老板压着我第一篇文章没发，这是最主要的原因，当然自己当时在搞申请，也有影响。
毕业后，我想把它扔了。
SUMMARY: The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. Four information content (IC)- and a graph-based methods are implemented in the GOSemSim package, multiple species including human, rat, mouse, fly and yeast are also supported. The functions provided by the GOSemSim offer flexibility for applications, and can be easily integrated into high-throughput analysis pipelines. AVAILABILITY: GOSemSim is released under the GNU General Public License within Bioconductor project, and freely available at http://bioconductor.org/packages/2.6/bioc/html/GOSemSim.html.
