At the same time, TU Delft has adopted a mandated green open access policy. This means that for papers published after May 2016, an author-prepared version (pdf) must be uploaded into Pure.
I am very happy with TU Delft’s commitment to green open access (and TU Delft is not alone). This decision also means, however, that TU Delft researchers need to do some extra work, to make their author-prepared versions available.
To make it easier for TU Delft researchers to upload their papers and comply with the green open access policy, here are some suggestions based on my experience so far working with Pure.
I can’t say I’m a big fan of Elsevier Pure. In the interest of open access, however, I’m doing my best to tolerate the quirks of Pure, in order to help the TU Delft to share all its research papers freely and persistently with everyone in the world.
Since Pure is used at hundreds of different universities, this post may also be relevant for researchers not working at TU Delft.
- The Outcome
- Accessing Pure
- Entering Meta-Data
- Entering your Author-Prepared version
- A Paper’s Life Cycle
- Updating Entries (Before/After “Approval”)
- Older (before 2015) Entries
- End-of-the-Year Publication Reporting
- Google Indexing
- Complicated Author Names
- Exporting To Bibtex
All pages have persistent URL’s, making it easy to refer to a list of all your publications (such as my list), or individual papers (such as my recent one on crash reproduction). For all recent papers I have added a pdf of the version that we as authors prepared ourselves (aka the postprint), as well as a DOI link to the publisher version (often behind a paywall).
Thus, you can use Pure to offer, for each publication, your self-archived (green open access) version as well as the final publisher version.
Moreover, these publications can be aggregated to the section, department, and faculty level, for management reporting purposes.
In this way, Pure data shows the tax payers how their money is spent on academic research, and gives the tax payer free access to the outcomes. The tax payer deserves it that we invest some time in populating Pure with accurate data.
To enter publications into pure, you’ll need to login. On https://pure.tudelft.nl, in the footer at the right, you’ll find “Log into Pure”. Use your TU Delft netid.
If you’re interested in web applications, you will quickly recognize that Pure is a fairly old system, with user interface choices that would not be made these days.
You can start entering a publication by hitting the big green button “Add new” at the top right of the page. It will open a brand new browser window for you.
In the new window, click “Research Output”, which will turn blue and expand into three items.
Then there are several ways to enter a publication, including:
- Import via Elsevier Scopus, found via “Import from Online Source”. This is by far the easiest, if (1) your publication venue is indexed by Scopus, (2) it is already visible at Scopus (which typically takes a few months), and if (3) you can find it on Scopus. To help Scopus, I have set up an ORCID author identifier and connected it to my Scopus author profile.
Import via Bibtex, found via “Import from file”. If you click it, importing from bibtex is one of the options. You can obtain bibtex entries from DBLP, Google Scholar, ACM, your departmental publications server, or write them by hand in your favorite editor, and then copy paste them into Pure.
Entering details via a series of buttons and forms (“Create from template”). I recommend not to use this option. If you go against this advice, make sure that if you want to enter a conference paper, you do not pick the template “Paper/contribution to conference”, as you should pick “Conference Contribution/Chapter in Conference Proceedings” instead. Don’t ask me why.
In all cases, yet another browser window is opened, in which you can inspect, correct, and save the bibliographic data.
With each publication, you can add various “electronic versions”.
Each can be a file (pdf), a link to a version, or a DOI. For pdfs you want to upload, make sure you check it meets the conditions under your publisher allows self-archiving.
Pure distinguishes various version types, which you can enter via the “Document version” pull down menu. Here you need to include at least the following two versions:
- The “accepted author manuscript”. This is also called a postprint, and is the version that (1) is fully prepared by you as authors; and that (2) includes all improvements you made after receiving the reviews. Here you can typically upload the pdf as you prepared it yourself.
The “final published version”. This is the Publisher’s version. It is likely that the final version is copyrighted by the publisher. Therefore, you typically include a link (DOI) to the final version, and do not upload a pdf to Pure. If you import from Scopus, this field is automatically set.
Furthermore, Pure permits setting the “access to electronic version”, and defining the “public access”. Relevant items include:
- Open, meaning (green) open access. This is what I typically select for the “accepted author manuscript”.
Restricted, meaning behind a paywall. This is what I typically select for the final published version.
Embargoed, meaning that the pdf cannot be made public until a set date. Can be used for commercial publishers who insist on restricting access to post-prints from institutional repositories in the first 1-2 years.
The vast majority (80%) of the academic publishers permits authors to archive their accepted manuscripts in institutional repositories such as Pure. However, publishers typically permit this under specific conditions, which may differ per publisher. You can check out my Green Open Access FAQ if you want to learn more about these conditions, and how to find them for your (computer science) publisher.
Making papers early available is one of the benefits of self-archiving. This can be done in Pure by setting the paper’s “Publication Status”. This field can have the following values:
- “In preparation”: Literally a pre-print. Your paper can be considered a draft and may still change.
- “Submitted”: You submitted your paper to a journal or conference where it is now under review.
- “Accepted/In press”: Yes, paper accepted! This also means that you as an author can share your “accepted author manuscript”.
- “E-Pub ahead of print”: I don’t see how this differs from the Accepted state.
- “Published”: The paper is final and has been officially published.
In my Green Open Access FAQ I provide an answer to the question Which Version Should I Self-Archive.
In particular, I do the following once my paper is accepted:
- I update my pdf with a (foot)note indicating where it will be published, and who will eventually hold the copyright.
- I create a bibtex entry for an
@inproceedings(conference, workshop) or
- I upload the bibtex entry into pure.
- I add my own pdf with the author-prepared version to the resulting pure entry
- I set the state to “Accepted”.
- I share the Pure link on Twitter with the rest of the world.
Once the publisher actually manages to publish this paper as well (this may be several months later!), I update my pure entry:
- I add the DOI link to the final published version.
- I provide the missing bibliographic meta-data (page numbers, volume, number, …).
- I set the state to “Published”.
My preprint links I shared still contain a pointer to the self-archived pdf, but now also to the official version at the publisher for those who have access through the pay wall.
A publication you entered can be in three states:
- “For Approval” means that the publication has not been approved yet by a TU Delft Library employee. It also means that you can still make changes yourself. This is the default state a publication is in once after you entered it yourself.
“Approved” means that a TU Delft library employee has approved the publication. This means that you yourself cannot change this publication anymore. If your publication does need a correction nevertheless, you will have to email the TU Delft library contact person for your department (Jasper van Dijck for my Department of Software Technology).
“Entry in progress”: This is a state you can use to indicate that you still plan to update the publication — it instructs the library not to try to approve the (intentionally incomplete) entry. In the life cycle discussed above, you could use this state to mark an entry as in progress between the acceptance of the paper (no DOI yet) and the actual publication (DOI available).
(These states can be configured differently for different Pure installations.)
Entries from 2015 and before were automatically imported from TU Delfts old Metis system (which in our Department of Software Technology in turn was populated from our ST Publication Server. Since Metis did not support pdf uploads, these older publications do not come with open access post-prints in Pure.
To update such older entries, see the updating procedure described above.
As any (Dutch) university, the TU Delft has to report to its stakeholders what its “output” is. This information is collected in Pure, and used by the government to analyze the research performance of various universities.
This means that in, say, February of year N, all publications in year N-1 must have been entered into Pure.
If you follow the Scopus approach (like I try to do), this means that due to the delay in Scopus you may have to switch to the bibtex approach to enter publications from November or December.
Note that in the United Kingdom under the REF open access policy, authors must upload their papers within 3 months of being accepted. The TU Delft has no such rule yet as far as I know, but this would simplify the process of end-of-the-year publication collection.
The TU Delft Pure data itself is not indexed by Google (as far as I know). The papers that I have uploaded into Pure are discovered by Google Scholar. This is in line with the harvesting objective of Pure:
Research output entered in Pure is harvested by Google Scholar and visible on that platform.
Note also that pdfs uploaded in Pure should be automatically (after validation by the library) copied to https://repository.tudelft.nl, which is indexed, meaning that your papers (and your post-prints) will end up in Google Scholar.
Pure contains official employee names as registered by TU Delft.
Some authors publish under different (variants of their) names. For example, Dutch universities have trouble handling the complex naming habits of Portuguese and Brazilian employees.
If Pure is not able to map an author name to the corresponding employee, find the author name in the publication, click edit, and then click “Replace”. This allows searching the TU Delft employee database for the correct person.
If Pure has found the correct employee, but the name displayed is very differently from what is listed on the publication itself, you can edit the author for that publication, and enter a different first and last name for this publication.
If you’re logged in, you can download your publication list in various formats, including BibTex (you’ll find the button for this at the bottom of the page).
I needed slightly different BibTex output in order to be able to import it into our local publication server, so I wrote a little Python script to scrape a Pure web page (mine, yours, or anyone’s), that adds relevant information (such as a
url field linking back to the paper’s Pure page).
- 20 November 2016: Version 0.1, for internal purposes.
- 07 December 2016: Version 0.2, first public version.
- 14 December 2016: Version 0.3, minor improvements.
- 13 January 2017: Version 0.4, updated Google Scholar information.
- 16 March 2017: Version 0.5, updated approval states based on correction from Hans Meijerrathken.
- 17 March 2017: Version 0.6, toc, life cycle and exporting added.
Acknowledgments: Thanks to Moritz Beller for providing feedback and trying out Pure.
© Arie van Deursen, December 2016.