Saturday, December 26, 2020

Wikicite: "No #rewilding in Wales" but why or why not?

No rewilding with a background of bracken

There is rewilding practice, there is rewilding science and there is rewilding controversy. Never mind how you define rewilding, it has been practices for a long time and rewilding practitioners want scientists to study the efficacy of their work. 

There are many papers that are about rewilding or touch on rewilding and as I am fascinated by rewilding, it is all too easy to concentrate on the papers and people that I like. So I am adding all the cited papers for "Abandoning or Reimagining a Cultural Heartland? Understanding and Responding to Rewilding Conflicts in Wales - the Case of the Cambrian Wildwood". The full text is available only as a PDF and as a consequence I have to google for every citation not yet in Wikidata. The result is a wealth of additional papers (they have a DOI), and new books etc have a mention on the Wikidata item.

As more papers on conservation, rewilding and its politics find their way in Wikidata, not only the Scholia for that paper evolves all the papers it touches have at least one "citing paper". The version of the tool that I use, SourceMD, is the first iteration of a tool that in a later iteration looked up authors from ORCiD ... Sadly no longer available. It has me use the author disambiguator to replace author strings with references to authors expanding the Scholia representations for authors and papers even more.

When you find scholarly papers interesting and you know what papers it cites, it should provide a mix op opinions balanced to make what is the point of the paper. At that it is comparable to a NPOV article in a Wikipedia. One provides original research and the other reflects on the available research.

What I do is in a wiki way.. When another paper takes my attention away, I leave a paper to eventually return to it. It is one reason why I work sequentially from top to bottom and add everything.

Thanks, GerardM

Wednesday, December 02, 2020

Wikicite from the ground up: attending a symposium on "rewilding"


Professor Dr Liesbeth Bakker has as a role to establish the science behind the rewilding practice. Professor Bakker has been appointed as the Special Professor of Rewilding Ecology at Wageningen UR in April 2020. Because of the Corona pandemic, her maiden speech is for now replaced with a one time symposium on the subject. Anyone can attend, it is wildly popular and you can attend to this one day event as well

Rewilding is being practices on a large scale, it did not happen overnight, there is a large amount of scholarly work that will be the basis of what Professor Bakker will consider in her own research.

What I can do for the occasion is make a Scholia for the conference? I can add more citations to papers, I can attribute papers to scholars. The bottom line for citations is that they are an invite to read more papers, to get to a better understanding of what is considered. Providing a better understanding of rewilding is the role Professor Bakker. When the public is to understand subjects like rewilding, ecology Wikipedia is the first place people go to. Its references can now link to Wikidata but from there it is still a huge step to a Scholia for a paper and better understanding of a paper.

When the subject matter of rewilding is to be more inclusively covered in Wikidata, it follows that the ecology of Wikidata has to play its role. It consists of items, properties and qualifiers. It has its data with  bots and users all iterating on. Applying this ecology for a purpose is a challenge.

As a paper like "Wild Steps in a semi-wild setting? Habitat selection and behavior of European bison reintroduced to an enclosure in an anthropogenic landscape" has no references in Wikidata, there is not much in its Scholia. Compare that to this paper where references exist to all the cited papers. Wikidata provides a rabbit hole that can help bring context to subjects, authors and papers. What to do for rewilding is very much a collective challenge.

Thanks, GerardM

Thursday, November 26, 2020

Wikicite from the ground up: understanding wildfires

The world has to deal with climate change and one of its effects is the severity of wildfires. One paper on the subject is "Can trophic rewilding reduce the impact of fire in a more flammable world?" It is only one paper, there are others. It caught my attention after watching YouTube about goats and blogging about rewilding..

When I found the paper, it did not have any "cites work" statements. In the PDF of the paper, references to 91 other works can be found. Text in a PDF is problematic; you may scrape the titles and search for a match but you won't find them in Wikidata even when they are there. This is because of missing spaces and special characters that are different in Wikidata. It has been a lot of work finding and linking many of the citations. 

The effect of these references on the Scholia for the paper is staggering. It demonstrates the power of open data; authors of the cited papers are shown, there is an accumulation of the papers they have in common. The associated subjects are shown and have their own weight. 

The papers informs that there are 91 cited papers, at this time only 54 papers have been linked. All of them have a title, a DOI. The Scholia presentation is the best we have for the paper but it is as a consequence incomplete. Why not have a "Cites work string"? Combined with attributes like "series ordinal" and "DOI" even "Main subject" it completes missing information for the paper. Bots can pick up on this, check Wikidata for the DOI, add the paper when we do not have it and even replace the string when it is with the process of checking and importing papers. 

When people take the effort of understanding a subject like "wildfires" and enrich important papers, the power of their work followed by the work done by bots opens up scholarly papers even more to the people who care to learn from the scholarly papers themselves.

Thanks, GerardM

Saturday, November 21, 2020

Wikicite from the ground up: a call to action

Many of the world's ecological systems are under thread. All kinds of reasons may be given and there is an interplay between the many causes that affect a downward spiral. Similar patterns can be found in many places and when these patterns are broken up, an ecological restoration may be one of the consequences.

I was called stupid when I said that water management is essential and suggested that beavers in California could do a lot of good. Beavers have been extinct in California for over 100 years, the many gullies in a watershed rush water straight to sea. Consequently the water table is not restored resulting is an increase in the risk of fires. So I am stupid, but at least I read some papers lately.

I follow the Mulloon Institute on Twitter, they have been restoring the watershed of the Mulloon Creek, this Australian project has been running for more than 10 years and apart from all the other benefits it restored profits to farmers by 60%. To underpin their results, they perform scientific research with the aim of convincing incredulous farmers and government to consider alternatives. This project is recognised by the United Nations as a research project. 

One of the papers they produced is about a possible reintroduction of the Green and Golden Bell Frog in the Mulloon catchment. I understand this paper to be about  an indicator species. From a scientific point of view, there are no issues, the paper is richly referenced and when you want to read scientific papers about the Green and Golden Bell Frog, check out its Scholia..

The problem is that like so many papers, it does not have a DOI and the best insurance for it being available in the future is the "Wayback Machine". It was not known there and it is now.. When papers are to be known to the general public, adding a paper like this to Wikidata is a next step

More can be done; for instance adding the references in the paper to the Wikidata item. Maybe there is an update about an introduction of the Green and Golden Bell Frog in the Mulloon Creek, who knows.. I did not find it.

Thanks, GerardM

Sunday, November 15, 2020

Wikicite from the ground up: references

When a point is made in Wikipedia, when a statement is made in Wikidata, best practice is to include a reference. The same is true in a scholarly paper, its references are typically found in a references section.

Wikicite is a project that brings many scholarly papers into Wikidata as beautiful as it is, it is a top down process. As an ordinary editor there is a lot that you can do to enrich the result.

The paper, "Can trophic rewilding reduce the impact of fire in a more flammable world?" has a DOI, the PDF includes a reference section. It takes a lot of effort to add the authors and papers it cites to Wikidata. The visibility of the paper improves and so does the visibility of the paper it cites. The Scholia shows that at this time, this paper is not used as a reference in Wikipedia. 

There is now a template that retrieves information from Wikidata for its reference data. It will be great when it is widely adopted because it provides an additional pathway from Wikipedia to the used references and the information relating to the reference.

So what can we do to improve on the quality of the data in Wikidata. First, the processes that import the bulk of new data are crucial, they are essential and need to be appreciated as such. The next part is enabling a community to improve the data. A recent paper explained what can be done with a top down approach. All kinds of decisions were made for us and the result feels like a one off project. 

When ORCID is considered to be our partner, it makes sense to invite people registered at ORCID to contribute to Wikidata. Their papers can be uploaded from ORCID into Wikidata, their co-authors and references can be linked by these people. As they do this while being logged into ORCID, we are assured because of their known personal involvement and use this as a reference.

The quality of such a reference is better than our current references that came with a link to an "author name string". Who knows that the disambiguation was correct? When a paper is linked to at least one known ORCID person with public information, we have a link we can verify and consequently it becomes a link we can trust. Once the link with a person with a ORCID identifier is established, we can ask to acknowledge the  changes that happen in his or her papers. Our quality is enhanced and a sense of community with ORCID is established.

Thanks, GerardM

Wikicite from the ground up: "Trophic rewilding"

In nature conservation, trophic rewilding and trophic cascades are important topics. When an animal like the howler monkey is no longer around, it no longer distributes the seeds of trees. The likely effect is that in time plants are no longer part of the ecosystem. Reintroducing a howler monkey restores the relation; it is considered an example of trophic rewilding.

At Wikipedia there is no article about trophic rewilding. As someone famously said, references are the most important part of a Wikipedia article, let's start with finding references.

There is a longstanding process of importing data about scholarly papers, all kinds of scholarly papers. Some of them have "trophic rewilding" in their title. Trophic rewilding was not known as a subject so it was easy enough to look for "trophic rewilding" and add it as a subject. Slowly but surely the Scholia representation evolves. More papers means more authors and more authors known to have collaborated on multiple publications. More citations are found for these papers and by inference they have a relation to the subject.

The initial set of data is already good enough to get a grasp of the subject but when you want more, you can look for missing data using Scholia, information like missing authors. The author disambiguator aids in finding papers for the missing author. With such iterations, the Scholia for trophic rewilding becomes more complete.

Another avenue to improve the coverage of a subject is by adding "cites work" in Wikidata for a paper like this one. Not all cited works are known to Wikidata but the effect can be impressive. NB The citations are often found in a PDF  and not in the article..

Slowly but surely all the scholarly references to be used for a new article are available, you can use a template in the article to link to the (evolving) Scholia. The best bit is you can add this template in an existing Wikipedia article as well providing a scholarly rabbit hole for interested readers.

Thanks, GerardM

Sunday, November 01, 2020

Wikicite from the ground up - oyster reefs


I watched this video having looked for oysters and oyster reefs. They are a thing in the Netherlands, we don't have them enough of them and should have them as a functioning ecosystem. 

The video starts with a Prof A. Randall Hughes moving into the water for an experiment. Prof Hughes was already in Wikidata from 2018. Being triggered by the video, adding additional information and papers is for me the thing to do. One of her paper is about oyster reefs, linking the paper to the item for oyster reefs includes her in the Scholia for oyster reef

Wikicite is about citations and one of its ambitions is to link Wikipedia references. There are many articles referenced that include the subject of the article: "oyster reef" but only one of them can be found in Wikidata. When you check the authors, Megan K. La Peyre is an associate Research Professor in the School of Renewable Natural Resources at Louisiana State University Agricultural Center, her name you will find quite often. It is cumbersome to add papers by hand, I made a stab at one of them. Only to find that I have to merge two items for Prof La Peyre because "there can be only one". 

Given that the scholarly papers among these references all have a DOI, we should have a tool that collects all DOI from the reference section of an article. It then gets the information from CrossRef using the DOI, includes the publication in Wikidata AND, something on my wishlist, link it to the Wikipedia article where it is used as a reference.

The objective of this tool is not so much expanding Wikidata but make it easy and obvious to find more information and publications on a topic through co-authors, subjects and Wikipedia articles where the same paper is used as a reference. When references are considered by some as the most important component of an article, it follows that it should be easy to expand from there in a whole different rabbit hole.

Thanks, GerardM

Saturday, October 31, 2020

Wikicite, but from the bottom up

Wikicite is one of the most active projects in Wikidata. Its purpose is to "develop open citations and linked bibliographic data to serve free knowledge". A lot of work has been done over the years, there is only one issue; what purpose does it serve.

One of the visible parts of Wikicite are the many Scholia presentations for information. Papers, authors, organisations, subjects even combinations. There is a template that enables the inclusion of Scholia information on a Wikipedia article like here.

One objective of Wikicite is to become the repository of all references of Wikipedia articles. This is where progress is possible enabling people like myself to combine the two and make it easier for Wikipedia editors to find even more sources.. I spend a lot of time adding the subject "trophic cascade" to scholarly articles that include the phrase "trophic cascade" in its title. In addition I attributed the papers of many a scholar as well. This is reflected in the Scholia for trophic cascade. Many of the papers in the references part of the English article are these same papers.

Referenced articles may be specific to multiple subjects and, may be part of the references of multiple articles. When we know all the papers used as references in a Wikipedia article in Wikidata, we can make the information in a Scholia even more useful. 

The information of existing papers with authors and citations can be enriched. For references we can add new papers., the subject of the Wikipedia article can be marked as a "main subject" for the paper as well. We weave a mighty web in this way. Our quality will be improved by flagging retracted papers and we can flag articles for an update when new information becomes available as well.

What we do does not have to be complete. That is not the way, that is not the Wiki way. When we start with what we have, we will find that it is already really useful.

Thanks, GerardM