Notes from Open Research London, 12 February 2024

Posted on February 27, 2024 by Frank Norman

Earlier this month Open Research London held a half day event at the Francis Crick Institute to mark Love Your Data week, comprising six half-hour talks. The very engaging and interesting talks were focused on research data discovery, with detours into publishing, preprints and AI. Attendees were well-supplied with coffee and pastries during registration and the halftime break, so there was plenty of time for chatting with fellow attendees. There was also an option to move on to a local pub afterwards to continue conversations and catch-ups. All in all, it was a great chance to learn from and discuss with knowledgeable people.

Here are some notes about each talk. I’ve put them in a different order from the actual programme.

  1. Dan Crane, from the Open Research team at King’s College

Dan started by describing the setup at King’s and outlining what FAIR data is (Findable, Accessible, Interoperable, Reusable). Then he outlined how his team capture datasets into the King’s Open Research Data System (KORDS) – a repository that uses FigShare.

The team at King’s have developed a metadata template to guide and encourage researchers to add descriptive metadata. There’s a balance to be struck between encouraging them to be as thorough as possible, whilst not nagging them so much that they are put off depositing their dataset. There’s also a balance between getting the researcher to do the work versus the Open Research Team taking on the work. I really recognise that dichotomy. Depositors in KORDS are encouraged to include a readme file and to add their ORCIDs. The system can also capture relationships between datasets. There is a good range of guidance and training material to help users to get their head around FAIR and open data sharing. Researchers are shown how they should reference the dataset deposited in KORDS when creating their data access/availability statement in the paper.

The King’s team also encourages researchers to create metadata-only records for datasets that cannot be shared openly, to give some exposure to this data.

Finally, Dan talked about how they create DOIs for grey literature in their PURE repository. Currently this is done manually. Guidance on ‘how to cite this’ is put on the page of each grey literature document that is posted in the repository.

I wonder how easy it is to get the message out to researchers that creating a DOI for any grey literature that they create is a Really Good Idea? I found that researchers (in life sciences at any rate) have a tendency to stick documents on general web pages without considering that there might be a better way to make them discoverable and accessible.

  1. Jonathan Green and Julie Baldwin from Univ Nottingham libraries

Jonathan and Julie described the process they use to find research datasets that have been deposited on external platforms by Univ Nottingham researchers, and then to import metadata from Scholix into the Nottingham repository. The aim is to create metadata-only records in the Nottingham data repository. Often research data is deposited into specialist domain repositories and thus is not easily visible or knowable via the university where the authors work. The Nottingham service is based on code shared by Durham/Manchester and uses the Scholix service as a data source.
Jonathan and Julie explained that initially they kept the project small-scale, due to resourcing constraints. The project started as an exploration – running some code to find what datasets existed ‘out there’ and then checking them manually before converting the metadata so it could be imported into the DSpace repository. The process has now been streamlined and further automated.

They had an interesting slide reflecting on some of the challenges and learning points. These boiled down to observing that the world of research data is messy, unpredictable and complex, hence human intervention is needed.

I found it very interesting to see this idea in practice as it’s something I’ve long thought could be useful. You can also import metadata from the EBI’s Biostudies database and I’ve seen this done, but for the purpose of research evaluation rather than for increasing the visibility of the datasets.

  1. Holly Ranger, from University of Westminster

Holly talked about capturing research outputs from practice research. This kind of research is often non-tangible, and collaborative, affected by its relations with other practice research. Holly noted that existing standards aren’t always suitable for arts research outputs. To improve the representation of practice research in the repository, Westminster has made various changes to the schemas for these. A particular feature is the ‘overlays narrative and context’. Holly said that contextualised data is really important for practice research. Holly mentioned persistent identifiers; RAiD, DataCite DOIs and CReDit. RAiD has proved to be a good fit for these outputs.

Westminster has embedded guidance to making practice research open within the practice PhD research handbook – explaining how to document the practice and research journey.

The second aspect of Westminster’s steps to embedding OA into practice research was implementing ‘Theory of change for research design’. I missed the details of this part of the talk. Holly mentioned the Practice Research Voices project, funded by the AHRC, and its final report and recommendations that have been published.

  1. Maria Levchenko, from the Europe PMC team at EBI

Maria talked about preprint discovery and preprint review/feedback, focusing on preprints in life sciences. She started with a definition of what a preprint is, and showed the growth in adoption of preprints and of preprint evaluations being posted. She mentioned that there are up to 60 preprint servers that have some biomedical content, and there are more than 35 initiatives reviewing life science preprints. This means that discovering preprints in life sciences can be challenging.

Europe PMC has been indexing preprints since 2018 and now has 735k preprints from more than 30 servers. Of those, 260k have been published in peer-reviewed journals and 10k have some kind of feedback.

Europe PMC also indexes preprint feedback and links them to the original preprint, to help readers assess the preprint. The feedback can be any kind of comment on the pre-published work. Though still small, the numbers of preprint peer reviews are now increasing. Researchers can gain exposure and credit through providing feedback on preprints. ePMC also links into funder and grant information about the research in the preprint, and citations to the preprint. These are all indicators of trust. Maria mentioned eLife’s Sciety website and EMBO’s Early Evidence Base website. Both of these categorise preprint feedback, but their categories are not the same. It would be helpful to harmonise types of preprint feedback.

Maria highlighted the issue of licences for reviews to whether and how the reviews can be reused. For example, can they be translated, text-mined, used by AI tools to provide summaries? Free to read does not mean free to re-use. Hence there is a growing need for pre-print licenses. Subsequently on Twitter EuropePMC posted:

If you want to be part of the conversations to define best practices and community standards sign up here: buff.ly/3uyZC3V

You can check for preprint updates using the Europe PMC Article Status Monitor tool to check if a preprint is:

  • Published in a journal
  • Withdrawn
  • Removed
  • Available as a newer version
  1. Mark Hahnel, Digital Science

Mark’s talk was titled “Global Academic Publishing: Where will experimentation lead?” He enumerated some of the qualities we look for in effective academic publishing: speed, openness, cost-effectiveness, trust. It’s hard to combine all four of these. Mark suggested that trust is the most important.

Mark sketched out some of the current problems in scholarly publishing: paper mills, research integrity failures, the volume of research that needs peer review. He pointed out that over the last 20 or so years the amount of academic research published has tripled, but there aren’t three times as many academics. Hence the peer review burden on each academic is increasing, and this is not sustainable. He asked whether/how we can limit the number of papers and datasets that need to be reviewed?

Mark said he doesn’t have answers to these problems, but emphasised that we need innovation in publishing in order to find the answers. He added that innovation can add complexity to the whole system, so it is not always welcomed by researchers/authors.

  1. Andrea Chiarelli, Research Consulting

Andrew talked about AI’s influence on open research discoverability and impact. He stated that there are many AI tools today and it’s hard to keep up. There’s even a website called ‘There’s an AI for that‘.

AI tools for enhancing search/discovery/review are getting better. Some tools can recommend what to read. Others can enhance research objects with machine-generated metadata, to improve discovery. Other AI tools can help to translate academic language into language that speaks to the policy and practitioner communities that can benefit from research findings. AI tools can also help with trend discovery and analysis.

Andrea highlighted three tools that are worth a look:

He acknowledged that there are drawbacks to AI. It’s a black box – leading to limitations in transparency and reproducibility. It’s difficult to understand the tools and language of AI. There is potential for bias and ‘hallucinations’ with generative AI. There are also data security and privacy concerns.
Finally, Andrea posed the question whether AI is a research partner or a research predator?

He presented the pros (research partner) thus:

  • AI becomes a powerful ally for researchers, enabling them to deliver more
    efficient, comprehensive and rigorous work.
  • AI tools help researchers with literature review, data analysis, hypothesis generation, experiment
    design and paper writing.
  • Researchers leverage AI to enhance their creativity, curiosity and critical thinking.
  • AI helps democratise research, making it more accessible, inclusive and diverse.

and the cons (research predator) thus:

  • Researchers lose their autonomy, agency and identity as AI takes over several facets of their roles.
  • AI enables a competitive and metric-driven culture, where researchers are pressured to publish even more and faster, sacrificing quality and integrity.
  • AI widens the gap between disciplines, institutions and countries, creating a monopoly of research by a
    few powerful actors.
  • AI tools are used to manipulate, plagiarise, and fabricate research results at scale by paper mills and toxic actors.

A question from the audience highlighted sustainability concerns with using free AI tools: who owns the infrastructure that we become depend on when we use these tools? What “hidden costs” are associated with this? This is an aspect that needs further thought by anyone building services that rely on these tools.

Posted in AI, Journal publishing, Open Science, Preprints | Comments Off on Notes from Open Research London, 12 February 2024

A choral coda

Posted on April 10, 2023 by Frank Norman

I have been singing with Crouch End Festival Chorus (CEFC) since late 1994 but I have now retired from the choir. The Rachmaninov Vespers on 31 March was my last concert with CEFC as a member. It will be quite a wrench after 28 years singing with CEFC but my voice is telling me it’s time to quit. This will be the first time in my adult life that I have not had a regular choir practice to attend each week.

I’m not giving up singing altogether: I will continue singing in my local church choir most Sundays, and I’ll still sing semi-regularly with a couple of other church choirs. These all entail turning up on a Sunday, rehearsing and then singing the service, so there’s no midweek rehearsal. I will also remain on CEFC books as a guest singer so I will receive invitations to sing with them on some occasions, but I won’t be a committed member.

Looking back

I didn’t do much choral singing as a child but in my later school years we had an enthusiastic head of music (Father Thomas Carroll) and I sang Handel’s Messiah, Haydn’s Nelson Mass and Mozart’s Coronation Mass when I was in the sixth form. This sparked my interest in choirs.

A quick trawl though my memory suggests that in the past 47 years since leaving school I have sung regularly with sixteen different choirs, plus quite a few more that I sang with briefly or sporadically, or joined for one-off performances. Sometimes I sang with two or three different choirs at a time so I had multiple rehearsals to attend every week.

Here are a few highlights of my choral career including music that was special and performance places that were special, choirs and chorus masters that made a significant impact on me, and some treasured experiences.

My first adult choir – Woking

After leaving school I worked for a year, living at home.  I joined a local choir – Woking Choral Society, conducted by Nicholas Steinitz.  He was the son of Paul Steinitz so had a good musical pedigree. This was my first experience of music making in an adult group. I was only there for a year but I treasure my first introduction to Bach’s St Matthew Passion (glorious) and I remember a luscious concert in Guildford Cathedral where we sang Faure’s Requiem and Rachmaninov’s The Bells. Everything I sang was new and exciting back then.

Getting into church music – Bristol

At Bristol University I sang in the big University choir and we performed Tippett’s A Child of our Time.  The music professor who conducted the choir had a correspondence by postcard with Michael Tippett and he read these out at rehearsals to encourage and inspire us. Then we were amazed when Tippett actually turned up at one of our final rehearsals. My parents came to the concert and found it very moving.

My most formative experience at Bristol though was singing church music. Soon after arriving in Bristol I went along to a service at Clifton Cathedral. It opened in 1973 and I loved the modern concrete architecture. After the service I introduced myself, saying how much I’d enjoyed the choir’s singing. I somehow found I was then invited to sing with the choir.

Clifton cathedral spire

Clifton Cathedral

Clifton is an RC cathedral but we sang music from Catholic and Anglican choral traditions. The high throughput of music of different styles, from Renaissance to 20th century, was a challenge, especially as it was all new to me. I’m not sure I was much use to the choir at first.  I recall Chris saying later that he barely heard me make any sound for the first year I was there! By the end of three years I could sight read pretty well and I had sung a huge amount of music.  As well as regular weekly services on a Sunday we sang occasional liturgical performances of some bigger works: Dvorak Mass in D, Durufle Requiem, Monteverdi Vespers, Rachmaninov Vespers (in Chris’s own English translation). I also remember a parish pilgrimage to Canterbury Cathedral. A chartered train took everyone from Bristol direct to Canterbury and we celebrated Mass in the Cathedral, with the Clifton choir singing. Canterbury Cathedral is a marvellous building, beautiful and full of history.  I remember staring up and marvelling at the beauty of the incredibly blue stained glass windows.

I left Bristol with a chemistry degree and some confidence in my singing ability.

More church music – Newcastle

I moved to the other end of the country and studied for a year in Newcastle, to get a PG Diploma in Librarianship. I joined the choir of St John’s, Grainger Street under Geoff Watson’s direction.  This is an Anglican church in the Anglo-catholic tradition so it didn’t seem such a big step away from the RC services I was familiar with. There was plenty of familiar music and many unfamiliar hymns. At St John’s I had my first experience of Evensong and of the peculiar magic of singing psalms to Anglican psalm chants.

Another strong memory of St John’s is the friendship I found there.  Joining a choir is a shortcut to gaining great friends.  After leaving Newcastle I met up with the St John’s people a few more times when they went away to sing the services in a cathedral for a week. We had great times and music in Lichfield, Southwell, Worcester and Chester.

A symphony chorus – London

I moved to London to start working as a Librarian.  One day I saw an advert recruiting for the BBC Symphony Chorus (BBC SC) and on impulse I applied and went for an audition. I didn’t really expect to get in but I did.  The BBC Chorus was a large symphonic choir, all amateur singers but with the resources of the BBC behind it.  The BBC SC was the resident choir for the BBC Symphony Orchestra. Now I was singing with a fully professional orchestra and with leading conductors.

At my first BBC rehearsal, in Feb 1981, I was thrown in at the deep end.  We started work on Berlioz’ Romeo and Juliet, in French of course with the choir divided in 16 parts. The second piece we rehearsed was Bartok’s Cantata Profana – in Hungarian and also in up to 16 parts. The Bartok piece includes a ferociously hard fugal section with the subject announced by the tenors on their own. Terrifying! I came to love this piece once I got to know it. Later that same year the Chorus travelled to Frankfurt to sing Britten’s War Requiem in a festival to mark the re-opening of the old Frankfurt Opera House, freshly refurbished as a concert hall. The symbolism of this (British choir, German orchestra, building partly destroyed in the war) was very moving. We were conducted by Eliahu Inbal, an Israeli conductor. He spent some time on rehearsing the chorus to sing incredibly quietly at the magic moments that Britten creates at the beginning and the end of the piece.

Royal Albert Hall

Royal Albert Hall

In my years with the BBC SC I sang plenty of choral repertoire, both the standard repertoire and much unusual music. We sang 10-12 concerts a year.   The BBC was dedicated to new music and I was happy about this. Working with Krzysztof Penderecki on his St Luke Passion was an extraordinary experience. At first I didn’t know what to make of the score but gradually he explained what we had to do and the powerful music came together. We also joined the BBC Singers in a performance of the very challenging Ligeti Requiem.  The BBC Singers often joined our concerts to sing any semi-chorus sections or just to strengthen the sound. They were brilliant. They sang most of the Ligeti on their own but the Chorus sang in a couple of movements. Another highlight was singing in the first UK performance of Tippett’s The Mask of Time at the Proms. This was a long and complex work that took a lot of rehearsal. The BBC SC  took part in several of the Prom concerts each year in the lovely Royal Albert Hall, including the Last Night of the Proms which was always a great occasion, like an end of term party.

Back then I must have been full of energy.  Not content with all the rehearsals for the BBC concerts I also joined a church choir. I was living a few miles from Greenwich and paid a visit to look around.  I saw an LP in a shop window, a recording that St Alfege church choir in Greenwich had made.  It looked good – the kind of church music that I’d sung at Clifton and in Newcastle – so I went along to a service the next Sunday. I was impressed – the choir sang Messiaen’s short piece O Sacrum Convivium beautifully. I figured if the choir could cope with Messiaen then it was a choir I’d enjoy being with. So I introduced myself and joined up. It was quite a wild ride – loads of great music and great friends and much jollity (i.e. beer). The musical life in Greenwich was lively, much of it linked to St Alfege church and the choir directors Philip Simms and Steve Dagg. I had the chance to join in various one-off concerts conducted by them. I remember singing in the London premiere of a sacred piece by John Tavener, as part of the Greenwich Festival. Tavener attended our rehearsal on the day of the concert and vividly demonstrated the ecstatic quality of singing that he wanted from the choir.  He came over as slightly crazy but very inspirational.

Desert songs – Riyadh

In 1986 I went to work in Saudi, leaving all this marvellous music-making behind. It was not long before I discovered that there was a choral society in Riyadh.  It was a bit underground, for expatriates only, and it rehearsed in the basement of a hotel where all the guests were expats. Once more the choir was a good route to friendships in a place that was quite alien in many ways.  Musically the Riyadh Choral Society was a world away from the BBC but I sang my first Carmina Burana there – in a large gymnasium accompanied by two pianos, brass and timpani. I also sang the lead male role (Frederick) in the Pirates of Penzance, a rare step for me into the theatrical limelight.

Choirs on tour

I returned to the UK in 1989 and moved to Muswell Hill in north London. I rejoined the BBC SC for a few years but then they switched rehearsal venue from Broadcasting House in central London out to Maida Vale.  Coupled with an increase in the number of rehearsals I decided this was too much for me and I left.

During the next year or three I did several one-off concerts with different choirs.  Once you were known as a reasonably reliable and competent singer your name got onto choir fixers’ lists and I had the chance to sing in several interesting places. I sang Beethoven 9 in Bremen, in Ghent and at the Edinburgh Festival. After the Edinburgh concert I went along to three different Fringe shows and followed up with a couple of pints in the Festival Club in the early hours. I travelled with the Tallis Chamber Choir to Ireland to sing Patrick Cassidy’s Children of Lir at the Kiltimagh Festival.  Kiltimagh is a (very) small town in County Mayo and this was their first festival.  We all felt like celebrities walking about the place. It was a small place where everyone knew each other so of course they spotted that we must be some of the festival performers and greeted us like we were stars. I sang Mendelssohn’s Elijah in the Leipzig Gewandhaus with the Nederlandse Vereniging (Dutch Handel Society). Mendelssohn had a strong connection with the Leipzig Gewandhaus Orchestra so this performance had a special resonance. I had sung with this Dutch choir a few times previously, including a memorable tour with them to Poland in 1985 to sing Handel’s Theodora. I sang in the premiere of John Tavener’s grand work Apocalypse at the Proms, and later in the Megaron concert hall in Athens – that was one of the best overseas singing trips I made. Apocalypse had some wonderful moments but at three hours was a bit too long. Finally, I sang with Pro Musica two years running: Berlioz Requiem in Le Chatelet in Paris, and Beethoven Missa Solemnis in the Barcelona’s Palau de Musica – a truly beautiful concert hall.

A local choir with ambition

The chorus master for Pro Musica was a certain David Temple. One Friday evening a year or so after the Barcelona concert I was in my local pub when a whole lot of people came in at once, including David Temple.  We recognised each other and I learnt that Crouch End Festival Chorus (CEFC) had recently moved their rehearsal venue from Crouch End to a school just round the corner from my flat. I had seen posters for CEFC concerts and they seemed to sing interesting programmes.  Now they had started rehearsing almost on my doorstep it would have been rude not to join up.  I went to a rehearsal and David auditioned me.  I had not prepared anything to sing so he told me to sing Happy Birthday! I passed the audition and became a member of CEFC for the next 28 and a bit years.

For a while I had been a fan of so-called minimalist music but had not sung any of it. My first CEFC concert included Michael Nyman’s Out of the Ruins, a moving and mournful piece written in memory of the victims of the Armenian earthquake. A bit later we sang various pieces by Philip Glass – I especially loved Vessels from his mesmerising film score Koyaanisqatsi. David Bedford’s Twelve Hours of Sunset was also a special piece, finishing in a blaze of glory. Arvo Part’s Credo was a highlight and the choruses from John Adams’ opera Death of Klinghoffer were dramatic and captivating.

Alexandra Palace

Alexandra Palace

The choir also sang in external engagements for concert promoters like Raymond Gubbay and was booked for recording sessions, often of film music. This proved a lucrative activity for the choir and helped it to grow and to perform in more prestigious venues. As CEFC’s reputation grew so the engagements to more interesting. We sang a few times for Ennio Morricone in concerts of his own music that he conducted. More recently we’ve taken part in film screenings with live orchestra and choir.  The Lord of the Rings was a memorable one – not least because we sang it five times in one weekend! We’ve also performed Hans Zimmer’s music a few times, with him and his amazing entourage. The technical side of his  performances is very impressive.

CEFC used to perform mostly in churches, then used the Barbican quite often but it now has a new home in the theatre at Alexandra Palace.  This is ideal as it is local to the area, not too large, and the theatre has an excellent acoustic.

Rock stars

In 2007 CEFC was invited to sing with Ray Davies at the BBC Electric Proms in the Roundhouse, and this started CEFC’s choral rock adventures. The following year we sang again at the Electric Proms, this time with Noel and Liam Gallagher and Oasis. We sang a few more times with Ray and his band, mainly old Kinks songs plus a few newer songs. In June 2010 we went down to Glastonbury and sang with them on the Pyramid stage.  That was galactic. Just a few weeks later we were in the Royal Albert Hall on the first night of the Proms to sing Mahler’s 8th Symphony. That combination of two highly contrasting concerts and venues, just a few weeks apart, is uniquely CEFC and was a high point for me.

We sang several times with Noel and his post-Oasis High Flying Birds group on their UK tours.  For these gigs with amplified rock bands we had to learn a new way to sing. We each had headphones and were individually miked up. The key thing was to produce a good sound, not to try and compete with the band on volume.  For the sound test before every performance we each had to sing a phrase on our own. I recall the terror of singing into the vastness of an empty Manchester Arena and hearing my amplified voice filling the space!

In 2011 we sang with Basement Jaxx and the Metropole Orkest. I’d not encountered this music before but came to love it. The show was very flamboyant – we were all dressed in white shirts and white trousers, with black sunglasses. Some of the soloists had very extravagant and colourful costumes.

The end

Thanks to all the choirmasters I’ve sung for and all the other choir members I’ve sung with. I’ve learnt so much from all of them. I’ve enjoyed all the singing and have many great memories of ravishing music and fun times socialising after the music was over.

Posted in Biographical, Music | 3 Comments

Library day in the life, Spring 2022 (part 2)

Posted on April 22, 2022 by Frank Norman

This post is an account of what I did at work for four days in Mar/Apr 2022. The idea is to give an impression of the range of tasks I engage in during my work as librarian at the Francis Crick Institute. I’ve included some reflections and mini-rants so it’s not just a list of actions.

I’ve done this a few times over the years – the last time was in 2018.  Previously I’ve covered five days in a single week but I have done it differently this time. I’ve stretched it out a bit and ended up covering eight days in total over a period of two months. The previous post covered four days in Feb 2022.

Wed 2 Mar 2022 in the Crick

I’m working in the Crick today and got in early as it’s going to be a busy day.

We had a subscription problem yesterday – an invoice payment problem. It is on the way to being sorted and the supplier had seemed satisfied with my response yesterday.  But today we’ve been cut off from the service; two users got in touch with me first thing asking what’s up.   I shot off some emails – one apologetic to the users and one pleading to the supplier.  A bit later, and to my relief, it’s all resolved.

We’re getting some posters printed for our lunchtime popup event but the person who was supposed to do it was unable to come in to work today dues to transport problems. Fingers crossed his colleague can print them for us. Yes he can!

Recently an aspiring librarian paid a visit, to shadow me for a day and learn about our work.  This was arranged through the excellent NLPN (New Library Professionals Network). The person who visited then wrote up her experience, and today I sent off a short paragraph to go with her write-up on the NLPN website.

I replied to an email from a researcher about a new paper they’ve had accepted.  The publisher changed the CC BY statement that he’d included in the manuscript and he wanted to know if that’s OK.  I know that this publisher does allow OA compliance via the Rights Retention Strategy (RRS), so I’m not too worried if the wording is not exactly that given by Wellcome, so long as the intent is clear. We will be able to deposit the author-accepted manuscript to PubMedCentral with a CC BY licence.

Then I grabbed a coffee.  On the way I saw one of the group leaders who sits on our library committee.  She is a member of the wider editorial board for a journal which causes us a lot of OA problems. She said that she’d raised the issue at the last editorial board meeting but another board member (from a different UK institution that also has core-funding from Wellcome) insisted that it’s not a problem for them.  Hence no action was taken by the publisher. This is really unhelpful. It really is a problem and has been for many years   I dashed off an email to Wellcome  to suggest they remind all their funded researchers about this journal. I emailed our group leader with Wellcome’s response, to let her know I’d taken some action and that I appreciated her efforts to bring about change.

Our popup event in the Atrium to promote Reading Corner went well.  We had a good deal of interest and some good conversations about books, science history, philosophy and EDI. It was a lot of work putting it on so I was very glad we got a good response.

I had some more meetings in the afternoon, then I left slightly early as I was singing some lovely music for Ash Wednesday later.

Wed 16 Mar in the Crick

I got in early today to prepare for the ITO Gathering later on, and for some other meetings taking place.

There was not much relevant for me at the ITO Standup today. I grabbed a coffee then  checked in with ResearchFish to see how the submissions were going.  The number of people still to submit is diminishing so it looks like we’re on target to be finished by tomorrow’s deadline. I chased one person who’s not made a start on their submission yet.

Then I went straight into a meeting about OA we’d arranged for the Crick African Network Fellows.  We explained what the Crick OA policy requires and what the LIS team can do to support the CAN Fellows with OA. They were zooming in from South Africa, Ghana and Uganda. There was a slight technical problem with the sound at our end so I had to talk through all the slides. About half the fellows attended but it was recorded so can be shared with the others. There were a few questions at the end.  It was worth doing – I think we learned as much from the CAN Fellows as they did from us.

At the LIS catch-up (in person) we talked about our next pop-up, about the ResearchFish campaign (the deadline is tomorrow) and about changes to our internal grant codes.

I had a 1:1 session with one team member. We talked through the next steps with journal subscriptions. We are still waiting for two deals for 2022 to be arranged. I hope that we can get at least one of them sorted before the end of this financial year, but I suspect we won’t.

Then I sat in on a meeting with ITO colleagues about a Cybersecurity issue.  I didn’t have a lot to contribute, just some minor typo corrections to the draft plan. Sometimes I surprise myself with some good suggestions, but this topic was a bit too far from my area of operation.

After lunch I made some last-minute changes to the slides for the ITO Gathering (a monthly informal meeting for all ITO staff) then launched into the meeting itself, all on Zoom. We were a bit short of content for this meeting, but it turned out fine with some really interesting talks and demos of new projects completed.

Then I had another internal meeting. The Tech Request Group considers new IT system requests.  There were a couple of interesting ones – both quite small in scope but it’s always instructive to see how my IT colleagues approach this kind of problem-solving.

Next was a face-to-face meeting with two people from our Biological Research Facility. They are starting to promote the ARRIVE guidelines at the Crick and to encourage Crick researchers to follow the guidelines when publishing research. This is in conjunction with the National Centre for the three Rs (NC3Rs). We talked about the challenges of persuading researchers to follow new sets of rules, and I mentioned some of the other initiatives under way (training programs, research integrity) as well as our own OA work.  I agreed that we would add a question about ARRIVE to our manuscript notification form, to help promote awareness.

Then I spent a bit of time updating my job description. I tried to flesh it out a bit more –to balance between specifying someone who can lead and inspire a team, but who also knows all about current LIS and scholarly communications issues, including bibliometrics, Research Data Management and archives.

My final meeting of the day was with the Director, Chief Operations Officer and Research Director to discuss some current open access challenges posed by the new UKRI policy.

Thur 17 Mar in the Crick

The ResearchFish submissions are almost complete. My colleague will chase the final few later this morning. We made an effort this year to give more support to those who were making their first ResearchFish submission. This seems to have paid off as there are very few last-minute panics this time.

My manager has revised the draft job description and improved it hugely.   I gave some feedback and we’ve now got a version ready to go. Next stop, HR.

I attended the webinar about the UKRI OA policy, all 2 hours of it.

I arranged to be working in the Crick today in case I had to go knocking on doors to remind group leaders about their ResearchFish submissions, but all of them have been done – before lunch!  (Except one person on leave for whom we’ve arranged an extension).  It’s our best ever – usually we’re chasing up until 4pm, the deadline.

I had a zoom meeting with my counterpart at EMBL in Heidelberg. We do this every now and then to catch-up, share experience and tips.

I drafted a letter to UKRI raising an issue with the new OA policy. I also emailed a couple of major publishers, following up previous correspondence with them about the new UKRI policy.  I’m trying to make sure they are aware of the implications.

I exchanged several emails with one of our suppliers, and one of my ITO colleagues, trying to get SSO integration set up for a product. I think we’re nearly there now, after some stumbles.

Then I spent some time working on new additions to our publications database. The team add new Crick papers to our Symplectic system each week and I have to do a quick double-check and verify them.  We put quite a bit of effort into curating new papers, and adding various metadata elements.  Mostly this is straightforward but some papers are more tricky, and I have to judge whether a paper should be counted as Crick work or not.

Fri 8 Apr 2022, working from home

I dealt with a query from a group leader about her publications.  The list on the external website was different from the list in our Symplectic system, and slightly different from her own list. I figured out why and explained this to her.

One of my annual tasks is to help generate a list of papers to be highlighted in the Crick annual review.  All 120 group leaders are invited to submit one of their papers that they consider to be a major advance and I collate these for someone else to choose from. I worked through the first batches of responses, collating them and acknowledging their emails.  A few group leaders had questions about the process.

Friday is often a good day for pushing longer-term projects forward. We are looking at possibly assigning DOIs to our core-funded grants, and I’m trying to see what other funders are doing about Grant DOIs. Cue some emails.

I sent a few emails about some other OA projects and answered a GL question about OA.

Yesterday I met with a few people from a publisher, interested to hear my thoughts on information seeking and use generally, with a focus on ebooks and protocols. We had a memorable conversation not least because they made no attempt to sell me anything! In my experience that’s rare with publishers. Today I sent some follow-up information linked to some of the things I’d mentioned.

I sent some more email follow-ups – arranging to chat about archives, about a financial database product, trialling a new(ish) AI citation search tool. I also responded to a request to purchase some research management books.

I tweeted and retweeted some interesting things.  I also contributed to a thread about OA in SpringerNature journals, and whether we could publish in compliance with UKRI. I was then a bit surprised to read an email from Jisc on this subject, very late in the day, with follow-ups on twitter. I know some of the backstory to this so it was interesting to see it play out in real time.

Finally I drafted some internal news items about our new OA policy, and about new journal/article search tools that are now available to Crick staff.

Just in case you’re interested, the job advert for my role is now online.

Posted in Libraries and librarians | Tagged | Comments Off on Library day in the life, Spring 2022 (part 2)

Library day in the life, Spring 2022 (part 1)

Posted on April 22, 2022 by Frank Norman

This post is an account of what I did at work for four days in Feb 2022. The idea is to give an impression of the range of tasks I engage in during my work as librarian at the Francis Crick Institute. I’ve included some reflections and mini-rants so it’s not just a list of actions.

I’ve done this a few times over the years – the last time was in 2018.  Previously I’ve covered 5 days in a single week but I have done it differently this time. I’ve stretched it out a bit and ended up covering 8 days in total over a period of 2 months. This post has 4 days and the next post gives an account of 4 days in Mar/Apr 2022.

Thurs 10 Feb 2022

Today I’m working from home.  I have a comfortable chair, a good-sized table, a laptop and an extra screen.  It’s not quite as good as the office layout in the Crick building but it’s OK.

I start the day by reviewing emails and answering them or forwarding as necessary. One was a confirmation from a publisher to say they’ve renewed our subscription.  I’m a bit perplexed why this has come in now – I thought it was already renewed in November! But these days nothing surprises me when it comes to journal subscriptions.

I also check in to Slack and review any messages. One message told me about a big new neuroscience project involving two Crick labs. And another mentioned the UKRI consultation about its EDI (Equality, Diversity & Inclusion) strategy. The Crick has had an enterprise licence for Slack for a few years and it came into its own when the lockdown struck. There’s a mixture of general channels and other channels linked to specific work areas.

Next I check that my VPN connection is active and then I check my calendar for the day. It’s going to be a busy one (which is why I’ve chosen to document it here).

I log into our finance system and approve an order.  This is an open access (OA) payment to an Elsevier transformative journal. I wish these article processing charges could be zero-rated for VAT, the same as books, journals and ejournals.

I emailed a publisher representative about one of our Read & Publish deals.  We had a slightly unusual (favourable) arrangement for the deal in 2021 and I’d assumed this would continue for 2022. Yesterday I realised that on renewal in January it has changed to a slightly less favourable setup.  I penned a (slightly begging) email to see if we can go back to the more favourable arrangement for 2022.

Success!  They came back quickly and said yes.

I received an email from my boss about a new collaborative agreement between a Crick research group and a University research group.  They will share data with each other but also want to share an Endnote library. My colleague is our expert in Endnote so I passed it to her to look into, but I raised some copyright considerations too.

Before lockdown we used to put on small, themed book displays and soon we will restart these. Each one has about 16 books, all on a single theme.  We’re creating two new displays – one on Lab lit (the genre of fiction set in real-world scientific labs) and one on pandemics (including flu, COVID and also vaccination). I choose the books, my colleague drafts a booklet with information about each book and then I edit that, adding a paragraph about the theme of the display. Today I worked on editing the Lab lit booklet.

Then I had my first Zoom call of the day – with my IT colleagues. The Library & Information Services team is part of the IT office (ITO).  There is a daily short meeting with all the ITO team leads to review any issues and give project updates. Much of what goes on in these meetings is not directly relevant for me, but it’s instructive anyway and being there means I don’t miss anything crucial. The meetings are often only 10 mins long, but can extend to 30 mins if required.

There was also some discussion about a project to create a digital data retention policy.  IT colleagues have been talking with their counterparts at another institute.  I make a note to contact the archivist at that institute to find out more.

Then I went straight into the LIS Team daily catchup on Zoom. We started these catchups when we were all working from home at the beginning of the lockdown.  Now we’re working in the office on some days, but we have different days in the office so it’s still useful to have a quick catch-up every day.

Today we talked about a journal Read & Publish deal for 2022 that we’re still waiting to hear about. I agreed to chase Jisc. I am nostalgic for the days when the year’s subscriptions were all sorted out well before January! These days it takes until the end of April to sort everything out.  We also talked about which books to include in the pandemics and vaccination book display.

Later I attended a Zoom call to hear a vendor tendering to provide a contract and licence management system. This is for a Crick-wide system, but managing (journal) licenses and contracts is a bit of a headache for us so I’m interested in this project. Today’s was the second vendor to present their system. It’s interesting how varied the systems can be.

I popped out of my flat to get lunch. Usually I stay in but I wanted to get some fresh air today.

Another Zoom call – the monthly ITO all-hands meeting.  This is a monthly short address from our boss to update us on developments in the department, with a Q&A session to follow. This month we learnt about upcoming changes to the ITO dept structure, some updates on Covid arrangements and an update on the results of the Crick’s 5-yearly review exercise.

In the afternoon I had a Zoom call with one of my team members, to talk about digital science tools.  Her post was originally designated as an early career position, so I have built in some learning & development activities. We aim to have 1 or 2 sessions per month to talk about some aspect of library & information services. It hasn’t been as regular as that, especially during lockdown but now we’re almost at the end of the planned series. For today’s session, on digital science tools, I focused on the Bianca Kramer/Jeroen Bosman work, plus something on electronic lab notebooks.

I wonder whether to share my notes from these sessions more widely, though some of what I say quickly goes out of date. Maybe it’s a project for after I’ve retired (this summer).

I’ve also been keeping an eye on discussions on the UKCORR email discussion list.  A post there yesterday interested me so I’ve been checking to see if there are any further responses.  There was another good thread today, about Transformative Journals and UKRI policy.

Coincidentally, I spotted new guidance on the Jisc website, which mentions TJs.   I’d been told some back that this would be coming but it’s good to have it officially. I thought I knew what it was going to say but looking closely at this guidance I can see it is quite confusing and not what I’d expected.

I had an email from a certain video journal publisher telling me that their ‘business model is changing’.  Usually this is code for ‘you’ll have to pay more’. I’ll need to have a careful look at this ahead of our next library committee meeting in April.

An internal news piece I’d written about our ‘Reading Corner’ appeared in the Crick weekly round-up. Reading Corner is a few bookshelves containing our general and historical collection of books. The collection has been in storage for a few years, and the only outings the books had was via the themed book displays I mentioned above.  Now some space has been found for us to show off more of the collection – we have new dedicated shelving to display about 400 books (half the collection). The LIS team are quite excited about this and we hope that the researchers will enjoy the new facility too.

I should perhaps explain that the Crick library service is almost entirely an electronic service with no physical space or physical collection on display before now.

Wed 16 Feb 2022

I’m working in the Crick building today, so I have an extra screen and also real-life colleagues to talk to.

As usual I start by catching up on emails and Slack messages. I’ve realised that our access to a journal archive is broken. This is an example of a problem that we were discussing with Jisc yesterday, so it’s quite timely. I email our Jisc contact to explain what’s happened.

One of our Group Leaders has an interest in novel funding schemes (and has actually got a few things running in quite a big way to trial new approaches to funding research).  I’ve been working to put him in touch with one of my external contacts who is working on different aspects of novel research funding methods.  I’ve made the link between them now, so I hope they have a useful discussion.

I join the daily ITO Zoom call.  There’s a mention of the forthcoming Technicians Week at the Crick, and talk about creating an ITO stall on one of the days, to highlight the work of ITO. We also heard about plans for easing the COVID restrictions at the Crick.

Next was the LIS catch-up – not on Zoom this time. All four of us are in the building today so we had a real face-to-face meeting.  I passed on some info from the ITO meeting just before. We also discussed plans for the Reading Corner popup next month (we will have a table down in the ground-floor atrium during lunchtime, to promote the book collection). We came up with some good ideas for the event.

We also briefly discussed ideas for a future ORCID popup.  This will be part of a longer campaign to promote ORCID and our Crick Research Outputs system.

In the afternoon I joined a Zoom call with someone from Open Life Science (OLS),  plus two Crick colleagues who work on open science projects. We learnt about the work of OLS, particularly the mentoring/training programs they run. These are over 16 weeks, about 2 hours per week. Each mentee must think of a project and they will discuss it with their mentor every 2 weeks.  In the intervening weeks there is a cohort (plenary) call when they hear experts talk on a particular topic. In these calls the participants can also share their experiences with others in the program. It’s an interesting approach to promoting open science knowledge.  We will need to think about who/how to promote OLS at the Crick, both to mentees, mentors, and potential expert speakers.

Just after lunch I host the ITO Gathering on Zoom. This is a monthly informal 60-min meeting for everyone in ITO. We start with a short quiz, then a talk from someone in the Crick but outside ITO, then team news, achievements, possibly a short talk or two on a technical topic, and finally an ‘open mic’ talk where an ITO member of staff talks for 10 mins on any subject they want to choose. It’s a regular spot to celebrate successes and get to know each other better. It’s been Zoom-only for the past 2 years but I hope we can do a real life meeting soon. I arrange the speakers and host the meeting. I’m always exhausted at the end of the meeting!

I had 1:1 meetings with each of my team members today.  We normally do this weekly to talk through issues and identify any problems I can help with.

Fri 18 Feb

I’d planned to write about today’s activities, but I was off sick today.  I felt rough yesterday and am still very tired today.  My lateral flow tests are negative so it’s not COVID.

Tue 22 Feb

I’m in the building again today.  Two of my team members are in too, with another of them attending the R2R conference – in person! It will be great to attend a real-world conference again.

I have quite a lot of catching up (emails etc) to do after my couple of days off sick. I missed a meeting with ResearchFish but my colleague handled it for me. It’s good to have colleagues who can step up when needed.

I followed-up with someone who had asked about copyright for an article he’d written that was now accepted – asking which box to tick.  We need to check up what he’s doing about the OA too.

I also responded to another researcher who had suggested  ‘If there’s no deal with the publisher then we can ignore OA, right?’  I had to disabuse him of that lovely notion.

After my usual morning routine of the ITO and LIS daily Zoom calls I attended another Zoom session for a company tendering for the contracts and licence manager system. It was interesting again.

Then I went to look at a pile of books that one lab wanted to discard. A handful were interesting and we’ll add them to our Reading Corner. The rest we will arrange for collection by Book Rescuers. Between various labs closing we have about 150 books to dispose of now.

I went downstairs to grab a coffee and bumped into our internal comms person. He agreed to send an update/refresh about Reading Corner. We’ve had a few questions from staff and realised our initial notice wasn’t clear enough, so I have revised it.

I gave some help to a colleague who is setting up our new OpenURL resolver.  The information about different journal packages is not always clear – what titles are included, and which version of the package we should choose. It’s more difficult when some packages are actually ‘pick’n’mix’, so the published list of titles in the deal doesn’t match those that we actually subscribe to. I’m looking forward to getting this set up.  it will also feed into Browzine and Libkey – two new tools we are adding.

This afternoon I had a catch-up with the new EDI manager at the Crick, to talk about LIS and EDI. It was useful. Although mostly the LIS just deals with science information, we do go beyond that into related areas that support science. EDI is a key area that I’ve always been keen to support.

I had a request from a contact on LinkedIn to look at an editorial she has written on preprints. I agree to give some feedback.

I received an invitation to join an advisory board – I replied that I would love to but I will retire in 5 months, so best that they find someone else.

An email from a publisher asks if I’d like to hear about some exciting new product they are developing. I’m not really enthusiastic, but say ‘Yes, tell me all about it’.

Thur 24 Feb In the Crick.

I’m feeling all kinds of emotions with the news this morning from Ukraine.

My team member who does most of our open access work is attending the webinar on the new UKRI open access policy. Later she updates us about what was said.

A question about MyAthens+ was passed to me – do we want to upgrade our Athens subscription (i.e. pay more) to include MyAthens+?  I suspect the answer is going to be ‘no’. The extra product seems to be a portal thing and we’re expecting Browzine/Libkey to do this job for us once we’re fully onboarded. My colleague is digging into this a bit more before we respond.

I received an email from someone I know slightly asking if I’d give an online talk about OA and open science to researchers, as one part of a regular series of webinars on research integrity and related topics. I agree to do it.

A few other emails on small matters – fixing one of our scientists to talk at next month’s ITO Gathering; emailing an ITO colleague with a list of developments we hope to see implemented around the way publications are displayed on the Crick website; emailing my edited version of the book display booklet on pandemics etc; agreeing payment terms for a big invoice; forwarding details to colleagues of a long-awaited Read & Publish deal; forwarding details of the disaster recovery plan for a software tool we’re subscribing to.

I also email a scientist who’s trying to sort out OA for his new article, but the journal is one that is rather difficult.

At the end of the day I attend the Crick lecture, which is given by Demis Hassabis from Deepmind.  He is mightily impressive, explaining the power of machine learning in a straightforward and clear way. I think it’s one of the most interesting science talks I’ve been to for a very long time.

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FAIR data in practice

Posted on January 26, 2022 by Frank Norman

Introducing the next Open Research London event, which will be about FAIR data. 

It’s easy to agree that making research data FAIR is A Good Thing. Of course research data should be Findable, Accessible, Interoperable and Reusable. But is it imperative that all research data should be FAIR? If not, how do we identify those subsets that do need to be FAIR? What exactly do we need to do at a micro level to ensure that our data is FAIR?

Realising the aim of FAIR data in practice is challenging – it can take time and resources – and the benefits to the researcher of making their data FAIR are not always apparent. It’s important therefore to minimise any barriers to making data FAIR.  Research institutions should put systems in place to make FAIR data easy to manage and should explain clearly to researchers what they need to do.

Top-down

Since the FAIR data concept was launched in 2016 there has been a great deal written and talked about it but mostly that has been pretty high-level. We are seeing more practical guidelines emerge but I believe we still need more concrete explanations for both institutions and researchers.

The EOSC Expert Group developed an overarching FAIR Action Plan, published in 2018, but stressed that there was also a need for individual countries to put in place national action plans for FAIR. The plan was called Turning FAIR into Reality and it talks about the need to create policies, build a FAIR ecosystem, develop researcher skills, provide repositories and craft incentives. It also emphasises the need for PIDs (Persistent Identifiers) and standards, and the importance of machine-actionable data management plans. Skills development was identified as a major gap to be filled.

Some of the presentations at the launch event have useful summaries if you want to learn more about the plan.

To me it all feels a bit high-level still. The plan doesn’t quite bridge the gap from the high-level ideals of FAIR data down to quotidian research practice.

Creating infrastructure

The FAIRsFAIR project (Fostering Fair Data Practices in Europe) is endeavouring to create “an overall ​knowledge infrastructure on academic quality data management, procedures, standards, metrics and related matters”, based on the FAIR principles.

It aims to supply “practical solutions for the use of the FAIR data principles throughout the research data life cycle”. I do like the sounds of this.  Its emphasis is on “fostering FAIR data culture and the uptake of good practices in making data FAIR.”

The project started in March 2019 and is due to complete this year.  Recently they released a  training handbook, coordinated by Claudia Engelhardt.

Institutions, publishers, repositories

The Montreal Neurological Institute (MNI) is the first research institution to dedicate itself to Open Science. Its director, Guy Rouleau, was interviewed about MNI’s approach to open science in Genome Biology in 2017. MNI provides  some practical guidelines on FAIR data for its researchers.

A recent article by JB Poline (from MNI and McGill University) and others in Neuroinformatics considers how organisations can work towards making new neuroscience data FAIR, and calls for increased international collaborative standardisation of neuroscience data to foster integration and efficient reuse of research objects.

Iain Hrynaszkiewicz and colleagues from PLOS recently published the results of a survey of researchers, quizzing them on their needs and priorities for research data sharing. Their article in Data Science Journal highlights the role of publishers and repositories and the importance of linking research data and publications.

Sharing data in a repository is key requirement for data to be FAIR. Repositories such as Dryad can help to spread awareness and best practice.  Dryad has a page listing Good Data Practices.

Researchers

Some researchers support FAIR data for ethical reasons. Philippa Matthews wrote in the Journal of Global Health in 2019 about the need for FAIR data in order to help overcome the health problems caused by Hepatitis B virus.

Questions.

As a service provider in a research institution, I have these questions about FAIR:

  • what do I need to put in place to support researchers?
  • what should I be telling researchers they need to do?
  • what skills do I need to ensure researchers have?
  • do I really understand what each of the components of F-A-I-R means?

The event

Open Research London is holding a free virtual event called FAIR data in practice on Tuesday 1 February 2022, 3-4.30pm GMT.

The event will be chaired by Iain Hrynaszkiewicz, Director, Open Research Solutions at Public Library of Science (PLOS) and hosted online by the Francis Crick Institute.

There will be four short talks followed by a Q&A and discussion.

The speakers are:

  • Jen Gibson (Executive Director, Dryad)
  • Philippa Matthews (Group Leader at Francis Crick Institute)
  • Jean-Baptiste Poline (Montreal Neurological Institute and McGill University)
  • Claudia Engelhardt (Göttingen State and University Library)

They will be joined in the discussion panel by James MacRae (Head of Metabolomics platform at Francis Crick Institute)

The event is free but please register at Eventbrite.

 

 

 

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Publishing incrementally – micropublications

Posted on September 3, 2021 by Frank Norman

Looking back and looking forward

I recently received a reminder that it was my 13th anniversary of joining Twitter. I signed up to Twitter as a result of attending the Science Blogging conference in London in 2008 where I heard how useful it could be. I’d heard about Twitter previously, but was not persuaded it would be useful to me.  Well, it has proved enormously useful over the years.

It was at that event I also first heard about Open Notebook Science – an idea that blew my mind.  It still feels pretty radical to consider sharing all your research results as they are generated, and not many researchers have followed this path. Maybe it’s still something for the future.

A report produced in 2019 by Elsevier and Ipsos MORI envisioned what the world of research will look like in 2029. They reviewed the literature and interviewed futurists, research funders, publishers, technology experts and researchers. The report makes interesting reading, with a number of possible scenarios outlined.

I don’t think it is any surprise that one of the conclusions about research outputs was that “the article structure is evolving and new forms will become the norm”.  But it’s instructive to note that many of their respondents expected that articles would become further atomized, breaking into standalone elements.

Science Matters

Ten years after I learnt about open notebooks, a publisher called Science Matters came to give a talk at my institute. Someone working for them had earlier been a postdoc with one of our researchers and he’d arranged for her to visit. Science Matters  at that time published two journals:

Instead of publishing stories, Matters and Matters Select publish single, validated observations, thus highlighting the fundamental unit of scientific progress – the observation.

After the talk I did discuss whether the institute should sign an agreement with Science Matters for unlimited publishing by our researcher. I decided against it. I couldn’t justify the upfront costs without clear evidence that this new publishing platform was something our researchers would be motivated to use. Also, the costs of publishing five single-observation micropublications seemed to work out higher than those of publishing one regular paper with five observations.

Sadly the Science Matters’ website has now disappeared from view and is only available on the Wayback Machine. Their Twitter account still exists but is silent.

Micropublications

Learning about Science Matters was my first introduction to what I now know to be micropublications. I’ve since seen other examples of micropublications – for instance Flashpub, Experimental Results (from Cambridge University Press) and microPublication Biology. These micropublication platforms are another approach to the early sharing of research results. They are less radical than open notebooks but still represent a bold move.  They will soon be joined by the new Octopus platform.

As I’ve explored the world of micropublications I have observed that the term ‘micropublishing’ seems to have a variety of meanings – see this Wikipedia entry – but I’m using the term ‘micropublication’ as it seems to be reasonably well understood.

A micropublication, also called a Single Figure Publication, is “a peer-reviewed report of findings from a single experiment”. You could say that micropublications are the ultimate in salami slicing – the least publishable unit of research.

Another term I’ve seen is ’nanopublication’ – basically a single statement such as “misexpression of DUX4-fl, even at extremely low level, can recapitulate the phenotype observed in FSHD patients in a vertebrate model” expressed in a formalised way.  For me this rather stretches the concept of what is a publication, but it seems to be a term used in the semantic web community.  A recent article by Fabio Giachelle, Dennis Dosso, Gianmaria Silvello provides a useful introduction to nanopublications in life sciences.

In theory

In a thorough exposition in 2014 Tim Clark, Paolo Ciccarese & Carole Goble laid out their ‘micropublications semantic metadata model’:

The micropublications model is adapted to the Web, and designed for (a) representing the key arguments and evidence in scientific articles, and (b) supporting the “layering” of annotations and various useful formalizations upon the full text paper.

The micropublication approach goes beyond statements and their provenance, proposing a richer model in order to account for a more complete and broadly useful view of scientific argument and evidence, beyond that of simple assertions, or assertions supported only by literature references.

This is a re-imagining of research outputs for the 21st century, designing them to build into a corpus of knowledge that is fully formalised and evidenced. It is quite a theoretical vision of a micropublication and I am not sure to what extent current micropublication platforms have been guided by this kind of theoretical approach.

In practice

A more pragmatic vision from Long Do and William Mobley in 2015 describes the Single Figure Publication (SFP) as a more manageable method to inform research. They define an SFP as:

consisting of a figure, the legend, the Material and Methods section, and an optional Results/Discussion section, reduc[ing] the unit of publication to a more tractable size. Importantly, it results in a markedly decreased time from data generation to publication. As such, SFPs represent a new means by which to communicate scientific research.

They also look towards a more structured corpus of scientific literature:

It will serve as a forerunner of the nanopublication, a modular unit of information critical for machine-driven data aggregation and knowledge integration.

Adoption

What will it take to see a large-scale adoption of single-figure publishing? Will researchers see micropublications as a quicker and more manageable way to keep informed about new results?  Or will they see them as a new fad in publishing that only ‘publishing types’ are talking about?

Richard Sever (co-founder of bioRxiv) at a recent meeting suggested that the latter was the case and said that he saw no evidence of strong interest from researchers in publishing single-figure publications.  Indeed many researchers are not aware of what exactly SFPs or micropublications are.

On the other hand, if ten years ago you had asked a typical biomedical researcher what they thought about preprints then I suspect you would have received a pretty blank (at best) or negative (at worst) response.

Perhaps SFPs will be mainstream ten years from now, whether on new publishing platforms or in existing journals.

Open Research London – 29 September 2021

If you want to learn more about micropublications, then you can register for a virtual event organised by Open Research London on Wed 29 Sept 2021, 3pm – 4.30pm (BST).

Titled “Micropublications: publishing science results piece by piece”, it will be chaired by Michael Markle, publishing director of F1000Research, with the following speakers:

  • Kaveh Bazargan, Director, River Valley Technologies
  • Paul Sternberg, Professor of Biology, Caltech; Editor-in-chief, microPublication Biology
  • Alexandra Freeman, Executive Director of the Winton Centre for Risk & Evidence Communication, University of Cambridge; creator of Octopus.
  • Nate Jacobs, Chief Executive Officer, flashPub Inc.
  • Michael Nevels, Reader in Virology, University of St Andrews; Chief editor, Life sciences, Experimental Results

Register via this Eventbrite page.

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Page charges and OA policies

Posted on June 11, 2021 by Frank Norman

Much of my time in the past 12 months has been committed to preparing for compliance with the Coalition S / Wellcome open access policies. Because we have core funding from Wellcome this means that all research papers submitted on or after 1 Jan 2021 must comply with their new OA policy.

So I have been buried in transformative deals, transformative journals and the Rights Retention Strategy, trying to ensure that these will work to make our research papers open and compliant with Plan S.

This work continues. The new policy only affects papers submitted on or after 1 Jan 2021 so we are just seeing more papers coming through for publication that need to comply with the new policy. And we are seeing a few cases where the publishers policies and practices conflict with what Plan S stipulates.  We are now at the stage when ’The shit hits the Plan’.

The key aspects, or high mountains, of Plan S requirements are:

  • CC BY licence
  • Immediate OA
  • No hybrid APCs (except for Transformative Journals or Transformative Agreements)
  • Rights Retention Strategy

But down in the foothills are some other issues:

  • No page charges
  • No colour charges

This week we’ve had a couple of examples where publishers have asked us to pay page charges.  I won’t name the journals as we are still working through the issues with them and I hope we may reach a positive result in at least one case. But these are examples of the uncertainties and unexpected quirks of publishing that give me sleepless nights.

 

My Tweet on the topic.

 

 

 

Case Report 1
This is a subscription journal from a major publisher with whom we have a read and publish deal. The article appeared in the publisher dashboard at the end of April and was published as OA on the website on 29 April. Sadly it is not yet in PubMedCentral, so that’s something else we need to chase.

On 9 June the publisher emailed the author to say that on acceptance of an article the authors are liable for page charges – $140 for each typeset page up to 10 pages and $200 for each page thereafter.

I recall that the publisher a few years back ditched all their page and colour charges  – if you chose the paid OA route for your article then there were no extra charges, so this email is surprising. It might be an error – perhaps a standard process was invoked that shouldn’t have been in this case. It doesn’t seem to be a society journal, so I can’t see a reason why this title should be different from the publishers’ other titles. This title is listed in the agreement we have with the publisher.

We have queried this with the publisher and are waiting to hear back.

Case Report 2
This is a subscription journal from a moderate-sized US learned society publisher – they have nearly 20 journals altogether. They do not offer a read and publish deal and have not chosen to become a transformative journal. I had read that they would accept the Rights Retention Strategy language, and would allow immediate CC BY deposit of the author manuscript into PubMedCentral.

Our author made a mistake in her dealing with the publisher and selected the paid OA option before telling us about the paper. The paper was published OA on 9 June.   We then explained to our author that we cannot pay an APC as this is a hybrid journal and our funders do not permit it. We contacted the publisher and they agreed to cancel the paid OA status for the article. In the next breath they explained that we were now liable for page charges – these are waived when an APC is paid.  And it turns out that the page charges due are quite high. The APC would have been $2500; the page charges will be $1800.

So, we can break the ’no hybrid APCs’ rule and make the version of record immediately OA, or we can pay slightly less to break the ’no page charges’ rule and make the author accepted manuscript OA.  Fortunately the Rights Retention Strategy declaration is included in the article.

We have responded to the publisher explaining that we cannot pay page charges, and emphasising that if they offered a read and publish deal, or became a transformative journal, that would be remove the problem. Otherwise we will need a page charge waiver. We’re waiting to hear back.

Nuclear option
An apparently simple next step would be to cancel publication of both papers. I call this the nuclear option. I do not think it is a realistic option.

As a librarian I try to avoid dictating to researchers where they can publish, though I strongly advise them to avoid one or two known problematic journals.

If an article has already been published in a journal, I am not prepared to say to an author that they should withdraw the article and submit it elsewhere.  I’m not even sure that would be ethical or possible.

All my fingers and toes are crossed in the hope that we can reach agreement with both publishers in a way that complies with our OA policies. Otherwise I will have to  ‘strongly advise’ that our authors do not publish in these journals for the time being.

Posted in Open Access | Comments Off on Page charges and OA policies

Preprints and science news

Posted on February 4, 2019 by Frank Norman

I’ve written before about preprints and science news. That blogpost was occasioned by the open letter last summer from Fiona Fox at the Science Media Centre on the subject, and the follow-up comment piece by Tom Sheldon in Nature. Mine was just one of several responses, most of which sought to defend preprints from the perceived attack. The discussion served to demonstrate that preprints have become an important part of the biomedical research publishing scene, albeit still a small part.

It seems to me though that there is still an unanswered question about how preprints and science reporting will co-exist. That is why I have organised a meeting this week for open Research London on this topic. The speakers will be Tom Sheldon, Clare Ryan, Robin Lovell-Badge, Teresa Rayon Alonso. Tom is from the Science Media Centre and leads their work on preprints.  Clare is Head of Media Relations at the Wellcome Trust – an organisation that is a strong supporter of open access and preprints. Robin is a senior group leader at the Francis Crick Institute who has extensive media experience and is on the advisory board of PLOS.  Teresa is a postdoc at the Crick and a preprint summariser at preLights; she co-authored a response to Tom Sheldon’s article.

I think it will be an interesting evening and there are still a few tickets left but you need to register.  The event will not be streamed but we aim to record it.

I think it’s an interesting topic as it’s new, but also quite an old conversation, or rather two old conversations that are coming together. There have been endless conversations about the value or otherwise of embargoes in science news reporting – I remember them going back to 2009 but I’m sure they go back further. There have also been endless conversations about peer review and whether preprints in biomedicine are a good thing – I remember them going back to 1999 but again they certainly go back further.

I would summarise the problem as a series of mutually incompatible premises:

  1. Science benefits from preprints (speeding up communications)
  2. Science benefits from news reports (keeping science in the public eye)
  3. Embargoes are necessary for good science news reporting
  4. Preprints are incompatible with embargoes

There are a few other issues involved, but to my mind these are at the core of the problem.

At this point I had intended to write a magisterial overview of everything written on the subject, but time has run out so I will just include a few pointers to other writings and discussions.

On embargoes

I first heard the arguments about embargoes during a discussion at the World Conference of Science Journalists in 2009, nicely summarised by Ed Yong. There was another discussion at their conference four years later.

In 2016 noted embargo-watcher Ivan Oransky gave a brief history of embargoes and suggests they are no longer useful, but Vivian Siegel maintained they were still needed.

A rather different idea for reforming science news reporting was suggested by John Rennie following the Science Online conference in 2011.

On preprints

Matthew Cobb Traces the history of preprints in biology back to the 1960s in a very thorough article in PLOS Biology.  I still remember the lively discussion that took place in 1999 following Harold Varmus’ E-Biomed proposal.  An addendum to the proposal provided responses to some of the key issues raised in discussion.

On preprints and embargoes

I started out by saying that the issue of how to reconcile preprints and embargoes was an unanswered question, but there has been some discussion of the matter.

The (US) National Association of Science Writers held a meeting last autumn, bringing together journalists, press officers and journal editors. The conversations were summarised in a Google doc. Avren Keating observed:

In the end, there were more questions raised than answers, though a couple of messages did surface. Journalists, it was argued, are moving faster than the PIO community in adapting to preprints. The audience also believed journalists should take the same skeptical rigor they use to judge preprints of newsworthiness and apply that rigor to peer-reviewed research.

The future is now: How science communicators can adapt to preprints

A post on the STEMPRA blog last year by Claire Hastings mulls over the issue and comes up with some possible solutions, though for my money her solutions have the flavour of trying to turn the tide back.

Another blogpost from last year suggests that “Journalists Need to Adapt to Preprints, Not Ignore Them“.

I suspect that there’ll be a good deal more discussion to come about preprints and embargoes. I hope the event on 6 Feb 2019 will be a useful forum for informed discussion.

Posted in Communicating science, Preprints | Tagged | Comments Off on Preprints and science news

Diversithon – some recipes

Posted on December 10, 2018 by Frank Norman

Recipe 1

It’s a simple recipe. Gather together some people who want to change the world. Put some inspirational speakers in front of them to get people fired up about diversity in science. Provide cakes and biscuits. Teach some basic skills in editing and writing for Wikipedia, then set them loose on a list of scientists who deserve, but don’t yet have, biographical articles in Wikipedia. The room ignites in a silent flurry of activity and two hours later the cakes and biscuits have been transformed into Wikipedia articles about scientists from black, Asian and minority ethnic backgrounds.

That’s what happened on 9 November 2018. Nearly 40 people gathered to hear our speakers and learn about Wikipedia. Yolanda Ohene (UCL) and Sara Essilfie-Quaye (Imperial) talked about their experiences as black women in academia and their desire to see much-improved diversity and inclusion in science. Jess Wade (Imperial) talked about how increasing visibility through creating Wikipedia articles about women scientists and BAME scientists really can change perceptions, and change the world. No-one hearing her speak can have been left in any doubt about this. (If you want to understand what I mean, try watching Jess’ talk at the Royal Society’s Research Culture conference last month. Her talk starts at 4hr 25mins and lasts for about 12 minutes).

Finally, Alice White (Wellcome) provided simple instructions for creating effective Wikipedia articles, and some tips on how the Wikipedia community works. She was a good teacher and people learnt quickly.

Recipe 2

I’m very keen on Wikipedia (WP), but I am a rather sporadic contributor. I was first introduced to WP editing in 2011, when I attended a workshop at the MRC. The following year I participated remotely in a Royal Society editathon, on Ada Lovelace day. Then in 2013 I helped organise an editathon at NIMR for women scientists, which gained some attention, and another smaller one in 2014.

I’ve been wanting to arrange a WP workshop at the Crick for a couple of years but lacked the spark to make it happen.  Last year I had a chat with Beatrice Mikuzi, the then chair of our PRISM network, for black, asian and minority ethnic (BAME) staff. She commented that wikipedia editathons for BAME scientists always seemed to focus on USA scientists.  That implicit challenge sewed a seed in my head.

This summer I went along to a women-in-science wikipedia editathon at UCL, and there met Jess Wade and Alice White. I tweeted about the event and then my fellow Crick open science enthusiast Martin Jones saw my tweet and commented:

I think @franknorman and @jesswade would make an amazing
dynamic duo for a future wikithon!!

Well, how could I refuse? The sparks from Beatrice and Martin united and Diversithon was born.  I got to work with Alice and Jess and set a date for the event, then I liaised with the new PRISM co-chairs Karen and Esther. They injected a ton of enthusiasm and organisational skill. Actually Esther and Georgiee (from the engagements team) took on most of the organisation work from then on – they were the real dynamic duo.

The second recipe for success then was: someone keen on Wikipedia, someone with a vision for BAME in science, someone to light a spark and someone to enthuse and organise.

Recipe 3

We came up with an initial list of names of BAME scientists and via Twitter invited people to add to it. Jess Wade used her extensive Twitter following to solicit more names, and in October we added more names thanks to Black History Month as many people were tweeting on the subject.

When it came to the day, 9 Nov, it was a relief to see people enthusiastically turning up to the event. I want to say that our speakers were the stars of the day, but on reflection it was the attendees who deserve the limelight. They absorbed the Wikipedia ways of working – getting to grips with notability criteria (especially for academics) and neutral point of view, and the guidelines for biographies of living people. Then our new editors started reading about the scientists they’d chosen to work on, becoming enthusiastic as they learnt about the achievements of these people.

By the end of the afternoon some articles had been created, or started, and I sensed that many new converts to Wikipedia editing had been won over. If we could have kept going into the evening I think some people would have gladly done so.

The pages created and page views can be tracked here  (though some of those listed were created at other events).  The BAME scientists who still need articles to be created are listed at the bottom of this page.

The most important recipe is also the easiest – make sure you have some good stories to tell about scientists of colour who have been overlooked in Wikipedia. It turns out that there are plenty of them, and their stories will inspire you to write about them.

Continuation

The case for more events such as Diversithon was driven home by this recent salutary reminder in Nature of the need to democratise knowledge.

We are planning to run another event in 2019, and other events are also planned at Imperial College and Cambridge Univ.

Posted in Communicating science, Wikipedia | 2 Comments

Tracking less tangible research outputs

Posted on November 18, 2018 by Frank Norman

When I spot a problem then I start wondering what the solution is. It might be a bottleneck in some workflow, or a process that requires excessive effort to achieve a small effect. So I feel that there must be some way to improve the situation. Sometimes I can find a better way, other times I’m defeated – I throw up my arms and say “sorry – can’t help!”

In those cases, I sit down and write a blog post about it. This is one of those.

If you receive a grant or award from a research funding body then they usually require you to make a report on what you’ve done with the funding and what research papers, other outputs and activities have resulted. Several UK funders use the ResearchFish system to record this information, or rather they ask researchers to put their information into ResearchFish.

In theory it’s a good idea – if you have funding from multiple funders and each of them uses ResearchFish then you only need to put the information in there once but all the funders can draw it down.

In practice researchers seem to uniformly hate making their ResearchFish returns.

My Institute has recently signed up with Symplectic and we are about to implement the Symplectic Elements system to manage our research information better.  It will have information about publications, about researchers, their funding and their activities. The system will interface with ResearchFish, and it will be possible to squirt bibliographic information from our Elements system into ResearchFish. This kind of information (about research papers) is well-structured and standardised (PMIDs, DOIs etc), so it’s reasonably straightforward to transfer it between systems.

When it comes to other types of research activity, achievement or output then these standards are much less well-developed, so it’s a lot harder to exchange metadata in a predictable manner. All of the research information system vendors we spoke to said they would struggle to exchange information about (e.g.) public engagement activities with ResearchFish because this information is unstructured.

The kinds of information I’m thinking of include things like professional memberships or honours, medals and awards, membership of journal editorial boards or scientific advisory boards, talks, lectures and public engagement activities.

This got me thinking – what can be done to improve the situation?  It’s a problem that all researchers must face.

I think that for journal editorships and editorial board memberships the information could be there in Publons – though I think their coverage is still relatively low. Perhaps publishers could feed through this kind of information into Publons more routinely?  Or publishers could expose this information on their websites in a way that could easily be harvested into an ORCID profile, or a research information management system (something like Symplectic Elements). Is there a reason this can’t be done?  Perhaps it just needs a standard to be developed?

Gathering information about membership of other boards would be more of a challenge.

We would also want to gather science outreach activities (talks, lectures, festivals) undertaken by researchers. I can imagine a relatively simple standard metadata format could contain most of the information. If event organisers could be persuaded to create a little package of metadata then they could either email it to the researcher undertaking the activity or make it available for harvesting.  The event details then could be added to an ORCID profile and/or a research information management system, eventually ending up in ResearchFish.

At a recent OA event I bumped into Laure Haak (Executive Director of ORCID) and shared my idle musings about all this. She told me that they have been looking at the same problem. She suggested that integrating ORCID with systems like Eventbrite could help and that gave me hope that there will be some developments.

I wonder if any other people are working on this issue? Perhaps Force11? Is it even possible? Is there an obvious solution I’ve overlooked?

Posted in Metadata, Research management | 1 Comment