Reply to Rod Page (having technical problems posting this at PeerJ PrePrints)

reply1.txt

Thanks for your feedback Rod. I really value it.

I don't pretend to have all the answers. All of the academic content discovery 
services are fairly murky about how they actually index things, 
as I'm sure you know (Google Scholar perhaps being the most open-ish about how it does things?).

> how comparable are PLoS and Zootaxa from the perspective of search engines?

I am not a search engine. I am a human researcher. Whether a paper is 
published in Nature, Science, PLOS ONE or Zootaxa, it is the same to me - 
this is a logical and defensible position. I get what you're asking but as 
I've never had a job at a search engine I'm afraid I don't have much insight 
there.

> you used a complete set of Zootaxa PDFs obtained from the NHM? 

yes, that information is in the paper. Metadata about those PDFs is in the 
supplementary materials on figshare. As you know I cannot easily 'prove' I 
had the full set of PDFs because copyright restrictions do not enable me to 
repost the entire dataset, publicly online. This would infringe the copyright 
of Magnolia Press. I can however repost the entire set of PLOS ONE articles 
analysed as they were all published under CC BY or CC0.

> articles that are both open access and behind a paywall?

Yes. This is acknowledged in the paper. Regardless of whether a paper is open 
access to the general public, it could still be privately indexed by content 
search providers & that private full-text indexing made available during 
search. Discoverability is not access. Paywalls can be made semi-permeable, 
allowing known IP addresses through e.g. Google Scholar's indexing crawlers 
and bots, whilst denying access to non-subscribers at other IP addresses.

> Perhaps a better question is how the open access subset of Zootaxa compares to PLoS?

I'm sorry if I didn't make the hypothesis I was testing clearer. I want to 
test the discoverability of articles (regardless of OA or not). Yes, it does 
seem reasonable to pre-suppose that open access articles might be advantaged, 
but until we prove that with data I can't just make that assumption. If you 
know of any other research that demonstrates superiority of discoverability 
of OA research (not citation, views, downloads) then please let me know, I 
should cite it in this paper.

> confounding different media (PDF versus HTML) with different degrees of access?

I agree. This could certainly be one of the causitive mechanisms of the 
observed low recall of Zootaxa in Google Scholar. The point is, the observed 
effect (poor discoverability in Google Scholar) is real regardless of the 
cause [You're welcome to dispute the data given in the tables, but since I 
did the searches only a few days ago I doubt the results have changed]. If 
the cause is that Zootaxa does not provide HTML, then the obvious solution is 
that Zootaxa should provide HTML full-text. Or just accept low 
discoverability in Google Scholar :S

> Did you talk to Zhi-Qiang Zhang (editor of Zootaxa)?

Yes. I emailed him this morning.

I'm very pleased Magnolia Press have recently adopted DOIs, are moving the to 
OJS platform, and have adopted the CC BY licence for hybrid open access 
articles. These are all good moves towards better publishing. Given the 
results here, perhaps they should also look at providing full text HTML or 
XML, to continue their progress. They are an extremely important publisher of 
taxonomy.

> You are making various statements about how you think search engines access 
content, it would be interesting to actually know.

I agree, and also feel uncomfortable about the lack of evidence but services 
like Scopus, WoK, MAS, MS *are* untransparent, proprietary, opaque systems. I 
can't really change that. I certainly see that as a problem. Academia sorely 
needs an open, transparent system of indexing peer-reviewed published content.

> ...there is a world of difference...

Yes. I agree there is vast difference in funding between fields. I'm not 
entirely sure that difference prevents Magnolia Press from publishing full 
text HTML on their OJS platform. Other, similar "shoe-string" (your words not 
mine!)  operations also produce full text HTML on OJS, albeit not quite at 
the scale of Zootaxa & Phytotaxa. But surely this research could be used as 
evidence to ask for more funding? Here is objective evidence showing that 
more money is needed to do more useful taxonomic publishing to maximize 
return on investment. (?)

Prior to this research I was not aware of anything (aside from cited papers 
on OA citation, downloads, views advantage) that proves with real data that 
publishing in PLOS ONE provides excellent discoverability of research (in 
Google Scholar), substantially better than at other journals. That's why I've 
published this. I think people need to know about this. I think it's 
important. Incidentally this paper doesn't directly test whether 
discoverability has anything to do with OA. That needs follow-up work to 
demonstrate. 

This is merely a first-pass demonstration that born-digital journal content 
can have substantially different discoverability in academic search engines, 
depending on where it's published (Making a conscious effort here not to 
overstate what I've done).