Update bioRxiv and arXiv citations as needed

[agitter]

Before resubmitting we should update preprint references for manuscripts that have now been published. The Manubot build reports arXiv manuscripts that are now associated with a doi. We'll need to check bioRxiv manually.

[agitter]

I'm extending this to note that these references need to be added to manual-references.json because of problems with special characters:

• [x] https://doi.org/10.3389/fgene.2014.00342
• [x] https://doi.org/10.1534/g3.116.033654
• [x] https://doi.org/10.2337/diabetes.54.suppl_2.S68 (no longer cited)
• [x] https://doi.org/10.1109/JBHI.2016.2633963

Greycite problems:

• [x] http://www.jmlr.org/papers/v9/vandermaaten08a.html
• [x] http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.231.3442
• [x] http://www.ijcai.org/Proceedings/16/Papers/403.pdf
• [x] http://www.who.int/classifications/icd/en/
• [x] https://www.cs.toronto.edu/~kriz/learning-features-2009-TR.pdf

arXiv updates:

• [ ] 1704.01155
• [x] 1704.03296

[souravsingh]

https://doi.org/10.3389/fgene.2014.00342 is now added to the manual references. I can now work on the rest of the references.

[agitter]

Edited to add Maaten2008_tsne (http://www.jmlr.org/papers/v9/vandermaaten08a.html) from #648.

[agitter]

@dhimmel I noticed the greycite is back up. http://www.jmlr.org/papers/v9/vandermaaten08a.html is now processed automatically, as was the new URL from #774.

[agitter]

@dhimmel when I built deep review locally I saw a message about published arXiv papers that doesn't appear in the Travis build:

## WARNING
arXiv article 1704.01155 published at https://doi.org/10.14722/ndss.2018.23198
## WARNING
arXiv article 1704.03296 published at https://doi.org/10.1109/ICCV.2017.371 — Proceedings of the 2017 IEEE International Conference on Computer
  Vision (ICCV)

That doesn't seem like a problem, but I hadn't thought about this possibility before. It may be a good practice to periodically clear the cache during a local build to check for arXiv updates.

[agitter]

We have be having a problem parsing http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.231.3442 https://github.com/greenelab/deep-review/blob/16809c82043f9f2540857afd58dc51215eba732e/citations.tsv#L519

I'm going to switch to a tag to see if that helps.

[agitter]

Closing this issue. I corrected all of the reference errors I found and don't plan to manually review all bioRxiv and arXiv citations to see if they have been published.