Springer Publishing

Tuesday 27 October 2015

Open Science Working List

academia.eduwww.academia.edu/ social network
altmetrics http://www.altmetric.com measuring scholarly impact
authorclaim http://authorclaim.org/ measuring researcher impact
citeulike http://www.citeulike.org citation bookmarking
crossref http://www.crossref.org article metadata search doi resolver
crowdometer http://crowdometer.org/
datacite https://www.datacite.org/ doi provider
depsy http://depsy.org measuring scholarly impact
faculty of 1000 http://f1000.com/
Fast Track Impact http://fasttrackimpact.com research impact
figshare http://figshare.com/ data repository
github https://github.com/ computer programming
Global Research Identifier Database (GRID) www.grid.ac database
google scholar scholar.google.com/ measuring researcher impact
hypothesis https://hypothes.is annotation organize collaborate
impactstory https://impactstory.org/ measuring scholarly impact
journal of brief ideas beta.briefideas.org/ journal
journalreview.org https://www.journalreview.org/
kudos www.growkudos.com research impact
mendeley https://www.mendeley.com/ citation bookmarking
microsoft academic search http://academic.research.microsoft.com/ measuring researcher impact
mozilla science lab https://www.mozillascience.org/
open access infrastructure for research in europe https://www.openaire.eu/
open knowledge https://okfn.org/ data repository
open researcher and contributor id http://orcid.org/ researcher identification
open science framework (OSF) http://osf.io research publishing framework
papercritic http://www.papercritic.com/ monitoring feedback and conversation
peerj https://peerj.com/
plos impact explorer http://altmetric.com/interface/plos.html scientific conversation impact
plum analytics http://plumanalytics.com/ measuring scholarly impact
public library of science https://www.plos.org/ library journal
publons https://publons.com/ scientific review
pubpeer https://pubpeer.com/
readermeter http://readermeter.org/ impact
researcherid www.researcherid.com/ researcher identification
researchgate http://www.researchgate.net/ social network
rio journal http://riojournal.com/ journal
Securing a Hybrid Environment for Research Preservation and Access, SHERPA http://www.sherpa.ac.uk repository development
sciencecard http://50.17.213.175/ measuring researcher impact
scienceopen https://www.scienceopen.com/ publishing network
scinote scinote.net electronic lab notebook
slideshare www.slideshare.net/
sparrho https://www.sparrho.com/ recommender search engine
the new reddit journal of science https://www.reddit.com/r/science/ journal
the winnower https://thewinnower.com/ journal
wikipathways www.wikipathways.org/
wikipedia https://www.wikipedia.org/
wiktionary https://en.wiktionary.org/
zenodo http://zenodo.org/ data repository

the content mine,contentmine.org,
journal of open humanities data,
science.ai
Scihub, http://sci-hub.io, http://sci-hub.cc
The open journal, http://theoj.org, 
Protocols.io, https://www.protocols.io
Pubchase, www.pubchase.com,

Monday 19 October 2015

PubPeer - Scientific Conversation



PubPeer, The Online Journal Club, is a program that is involved in carrying on the conversation of science, mostly after work has been published.

Nuts and Bolts

Essentially, it appears to work by searching articles based on DOI or other unique identifier (e.g. PubMed ID) through the PubPeer interface. Once the article is found, you can provide comments on it.

Getting started

You become a member by inputting the DOI of a paper you published, selecting which author you are, then providing your institutional email address. ResearchGate is another service that requires an institutional email address to get started.

Providing Commentary

Of course there are guidelines on how to provide appropriate commentary through PubPeer.

The Browser Extension

I, as a good scientist, installed the browser extension. I tried it out searching the keyword "naphthenic acids". No PubPeer results on the first page. I also searched "cancer", "pubpeer" and "metabolomics" and there was no PubPeer commentary on any article on the first page.

Finally, I went to the PubMed featured comment for the day (Oct. 2, 2015) and saw the following page. The yellow bar above the article title shows how many comments are on PubPeer.



To access the PubPeer comment, you click on the white words "1 comment on PubPeer". You are then taken to PubPeer's webspace to explore the comment. The comment at PubPeer is pretty much the same comment below the article in PubMed Commons.






Commenting

I posted my first comment on PubPeer concerning an article about the synthesis of yaku'amide. This is how it looks!






Future

Will they permanently archive commentaries and/or commentary chains with DOIs? What is the difference between PubPeer and PubCommons in PubMed? How is PubPeer different than Disqus?

I know there are subtle differences, but I am still waiting to hear back from those organizations. Until then, PubPeer remains another excellent tool for scientific commentary just waiting to explode!

Monday 5 October 2015

Sparrho - Scientific Recommendation

Sparrho Logo

Sparrho ("sparrow") is a scientific recommendation service.


When I began playing with Sparrho, I got the feeling that it was similar to Google Scholar, but I knew it was different. I just couldn't tell how.


So I asked Sparrho myself!





Thanks so much! I also got an invitation to receive some "sparrhoswag". I'm not sure what it is, but it sounds good. Now I am trying to navigate sparrho.

--

Be it known that I am obsessed with naphthenic acids in oil sands process waters!

How can sparrho help me?

--

Well, the interface is sleek-looking, purple and starry! I am looking into a fascinating world. As I type in and save keywords, I am building a repertoire of articles of which I can mark as relevant (checkmark) or irrelevant (X) for my purposes. It's like I am building a research topic channel. I can immediately share articles over a variety of networks and link to the location of the article online.

The only thing is the 1D, 2D, 3D network graph logos that confuse me a bit.

THIS is how Sparrho is different from Google Scholar.

Line
The 1-D graph image is a search which contains only the exact keywords you've entered for your channel.

Square    The 2-D graph image search includes keywords defined as a more general concept. Here is where you want more and more keywords to give a better overall context for the research.

Cube    How could it get better than that? Well, the 3-D graph image represents Sparrho recommending new articles you didn't think you would need!

Okay, let me go back to Sparrho then and play the game!



The Game



 A 1-D search for the keywords "naphthenic acids", "OSPW", and "oil sands" gives 75 hits. By the way, these 75 hits are mostly research that has been published in 2015. The oldest articles in this channel are 2012.


A 2-D search returns over 400 hits! Excellent. I tend to get hits concerning various aspects of naphthenic acids chemistry: biodegradation, toxicity, structure determination, etc. Extremely useful. If an article is currently considered "noise" to a channel, I can mark it as irrelevant. I can also dig up the articles I have marked by clicking HISTORY button on the top right. I can change the status of an article to which I have already applied relevance status (for that particular channel).


A 3-D search produces 261 hits, which is less than 403, but doesn't mean the search has somehow failed. On the contrary, it succeeded by returning exactly the number of results it is supposed to return for the keywords and relevance scores supplied! Perhaps it suggests that my channel's keywords are quite 'directed' and do not have a diffuse set of connotations or definitions. I saw here some articles related to climate change and the Athabasca oil sands, as well as articles concerning oil sands soil nitrogen availability, and honouring indigenous treaty rights.

When you click on the information about an article, a pleasant green window pops down underneath called "People who read this also read", showing articles that can be called as such.



Summary

I am very excited to learn how to use Sparrho more effectively. I can envisage the 3-D search being extremely useful for academics who are charged with research that is very nebulous, publicly involved and has a lot of angles by which to approach: In fact this is all PhD projects, no matter how pessimistic you may feel! Using Sparrho can open you up to new research that is still directed toward your primary research interests and goals! Although I am developing analytical methods to characterize naphthenic acids, my efforts are directly related to policy and the wider industry. I believe it is my job to understand and be able to effectively manage the milieu in which my research is situated so I can have an impact there. Sparrho is helping.

P.S.: sparrhoswag?