publishing
Biodiversity informatics
26-08-2010 10:23
Bioinformatics, or more
precise, biodiversity informatics, is an emerging
field in which much progress already has been made.
However, overarching scientific questions seem to be
absent and therefore major, guiding goals are
missing.
In a recent review, Townsend Peterson et al. (2010) have tried to bridge this gap by posing a number of Big Questions.
According to these authors, “biodiversity science in general can and should evolve from a purely descriptive cataloguing endeavour into a predictive, scientific exploration of space, time and form”. This seems only logical.
This figure presents a framework of biodiversity informatics data realms, showing potential cross-links between some of them that are currently unlinked.
Given this framework the following areas of analysis could become available.
1. Geography and ecology of past life.
This topic is part of global change biology and seems to be very important when we try to anticipate biotic responses to future environmental change and biodiversity loss. The interaction of intrinsic and extrinsic factors on species’ responses remains little known.
2. Biota-wide picture of diversification and interaction
Community ecology currently focuses on closely relatives or known mutualists. However, a broader perspective is needed, leading to a more integrative view of both biotic interactions and biological diversification. Phylogenetic frameworks, geographic distributions and species niche estimates are key elements. This could result in insights incorporating ecological dimensions and likely shifts in distribution during historic times.
3. Future (novel) communities
Palaeontological evidence shows that in the past communities existed differing from extant counterparts. The shifts in novel species assemblages due to changing climates and the introduction of alien species may need further developments in niche modelling, leading to environmental change scenarios and future distribution predictions.
4. Integrating phenotype and genotype
Linking rich biodiversity data sets on phenotypes and genotypes of individuals, populations and species could be integrated over space and visualized in various dimensions. This would provide a view on how phenotype and genotype interact with geography and ecology.
5. Synthetic conservation planning
Only recently, conservation planning involves prioritizing using multi-factor, multi-temporal scenarios, which have the potential of covering more of the true complexity. This could lead to a more synthetic and robust view of conservation and nature resources management.
Some the key next steps involve data integration across disparate databases, data quality assurance, detecting errors and avoiding pseudoreplication, and finally, dealing effectively with scale.
All this - and more details in the paper - provides a challenging outlook. Undoubtedly, biodiversity informatics will become Big in the (near) future. But for me the key question is: what is the taxon involved? Having seen various incidents where people loose sight of the organism at stake, and focus instead on methodological questions and techniques to be used. “It’s the taxon, stupid”; even if this involves a purely descriptive cataloguing endeavour...
Reference:
Townsend Peterson, A., Knapp, S., Guralnick, R., Soberon, J. & Holder, M.T., 2010. The big questions for biodiversity informatics. - Systematics and Biodiversity 8: 159-168.
In a recent review, Townsend Peterson et al. (2010) have tried to bridge this gap by posing a number of Big Questions.
According to these authors, “biodiversity science in general can and should evolve from a purely descriptive cataloguing endeavour into a predictive, scientific exploration of space, time and form”. This seems only logical.
This figure presents a framework of biodiversity informatics data realms, showing potential cross-links between some of them that are currently unlinked.
Given this framework the following areas of analysis could become available.
1. Geography and ecology of past life.
This topic is part of global change biology and seems to be very important when we try to anticipate biotic responses to future environmental change and biodiversity loss. The interaction of intrinsic and extrinsic factors on species’ responses remains little known.
2. Biota-wide picture of diversification and interaction
Community ecology currently focuses on closely relatives or known mutualists. However, a broader perspective is needed, leading to a more integrative view of both biotic interactions and biological diversification. Phylogenetic frameworks, geographic distributions and species niche estimates are key elements. This could result in insights incorporating ecological dimensions and likely shifts in distribution during historic times.
3. Future (novel) communities
Palaeontological evidence shows that in the past communities existed differing from extant counterparts. The shifts in novel species assemblages due to changing climates and the introduction of alien species may need further developments in niche modelling, leading to environmental change scenarios and future distribution predictions.
4. Integrating phenotype and genotype
Linking rich biodiversity data sets on phenotypes and genotypes of individuals, populations and species could be integrated over space and visualized in various dimensions. This would provide a view on how phenotype and genotype interact with geography and ecology.
5. Synthetic conservation planning
Only recently, conservation planning involves prioritizing using multi-factor, multi-temporal scenarios, which have the potential of covering more of the true complexity. This could lead to a more synthetic and robust view of conservation and nature resources management.
Some the key next steps involve data integration across disparate databases, data quality assurance, detecting errors and avoiding pseudoreplication, and finally, dealing effectively with scale.
All this - and more details in the paper - provides a challenging outlook. Undoubtedly, biodiversity informatics will become Big in the (near) future. But for me the key question is: what is the taxon involved? Having seen various incidents where people loose sight of the organism at stake, and focus instead on methodological questions and techniques to be used. “It’s the taxon, stupid”; even if this involves a purely descriptive cataloguing endeavour...
Reference:
Townsend Peterson, A., Knapp, S., Guralnick, R., Soberon, J. & Holder, M.T., 2010. The big questions for biodiversity informatics. - Systematics and Biodiversity 8: 159-168.
SimpleMappr
30-03-2010 18:54
When you want to make a map with localities for a
paper or presentation, you often end up using rather
complicated methods involving several steps.
Today I found what seems to be a simple solution: SimpleMappr.
It is web-based map-making software, highly configurable and very easy to use. After a short test I think I’m going to love this one...
Today I found what seems to be a simple solution: SimpleMappr.
It is web-based map-making software, highly configurable and very easy to use. After a short test I think I’m going to love this one...
About IFs and the funding of taxonomy
04-02-2010 18:26
A colleague draw my attention to the following article that seems relevant for all those taxonomists out there who are struggling against the terror of Impact Factors and are wondering why taxonomy is such a discipline in decline in the Year of Biodiversity.
Research
policies ensuing from the Convention on Biological
Diversity made huge funds available to study
biodiversity. These were mostly dedicated to projects
aimed at providing services to taxonomy via
information and technology, or to develop “modern”,
i.e., molecular, approaches to taxonomy. Traditional
taxonomy was overly neglected and is in serious
distress all over the world. It is argued that both
novel and traditional ways to study biodiversity are
essential and that the demise of traditional taxonomy
(based on phenotypes) in the era of biodiversity is
the result of an unwise policy, mainly fostered by
portions of the scientific community that aim at
taking total advantage of the funds dedicated to the
study of biodiversity.
BTW: Interesting journal in which this paper
appeared...
Reference:
Boero, F., 2010. The study of species in the era of
biodiversity: a tale of stupidity. Diversity
2: 115-126.
Open access
06-01-2010 12:42
For those of you
interested in the ongoing debate on open access
publishing, the Open Access News
might be a good
source to keep on track.
The Scholarly Publishing and Academic Resources Coalition (SPARC) issues a newsletter, of which the latest issue summarizes the advancement during 2009.
The Scholarly Publishing and Academic Resources Coalition (SPARC) issues a newsletter, of which the latest issue summarizes the advancement during 2009.
Useful links
21-12-2009 11:54
One of the persons I
met last week in Portugal was Dora Lange Canhos,
director of the Centro de Referência em Informação
Ambiental, CRIA (Reference Center on
Environmental Information). It is a Brazilian
not-for-profit NGO aimed at a more sustainable use
of biodiversity through the dissemination of high
quality information.
One of the CRIA projects is SpeciesLink, a distributed database that integrates information from biological collections. I mentioned it before. Currently restricted to Brazilian collections, it plans to widen its scope and hope to encompass all collections related to the Amazon Basin. Maybe, also the Suriname collection in Naturalis will be integrated in this system; this collection is currently being digitized.
When I did the ‘Bulimulidae check’ I found 225 records listed.
There is a possibility to plot the data on Google Maps.
CRIA also publishes two journals. Biota Neotropica is an open access, tri-lingual journal on conservation and sustainable use of biodiversity. It is published online.
Checklist is a quarterly journal that publishes occurrence lists, geographic distribution maps and notes on the geographic distribution of taxa. It is also published online and open access.
So far, each of both journals has published only two molluscan papers (both on non-terrestrial snails). And although the relevance for Neotropical malacology of these journals is limited, I hope that in the future also papers on land snails will be published.
One of the CRIA projects is SpeciesLink, a distributed database that integrates information from biological collections. I mentioned it before. Currently restricted to Brazilian collections, it plans to widen its scope and hope to encompass all collections related to the Amazon Basin. Maybe, also the Suriname collection in Naturalis will be integrated in this system; this collection is currently being digitized.
When I did the ‘Bulimulidae check’ I found 225 records listed.
There is a possibility to plot the data on Google Maps.
CRIA also publishes two journals. Biota Neotropica is an open access, tri-lingual journal on conservation and sustainable use of biodiversity. It is published online.
Checklist is a quarterly journal that publishes occurrence lists, geographic distribution maps and notes on the geographic distribution of taxa. It is also published online and open access.
So far, each of both journals has published only two molluscan papers (both on non-terrestrial snails). And although the relevance for Neotropical malacology of these journals is limited, I hope that in the future also papers on land snails will be published.
Scratchpad training
17-12-2009 11:04
Taxonomy is a science
with an enormous task and limited capacity. Estimates
are 4-6000 taxonomists worldwide, 30-40000 amateurs
that are involved in a professional way, plus an
unknown number of citizens that are interested in
natural history. Moreover there is a mismatch between
the potential for web-based taxonomy and the
technological and management resources available.
Here comes in Scratchpads...
Scratchpads specifically enable community efforts and allow data to be uploaded and tagged in an intuitive way. The published data can be easily reviewed and maintained by the community, e.g. a group of collaborators.
This potential for sharing and building data made me decide to start using a Scratchpad. Hopefully, some of you will join me in this new way to participate in science.
See here, for more details on Scratchpads and what they are all about.
Functionality that I personally like are modules for bibliography, image galleries, phylogenetic trees, character matrices (under development), distribution maps. Also functionality is available for web fora and newsletters (both with email integration) and user blogs.
After an intensive day of training I have updated the Orthalicoidea site at several points. Have a look yourself!
Needless to say that this will always be a work in progress, evolving slowly, but hopefully steadily...
Reference:
Sarkar, I.N., 2009. Biodiversity Informatics: the emergence of a field. BMC Bioinformatics 10 (Suppl. 14): S1
Scratchpads specifically enable community efforts and allow data to be uploaded and tagged in an intuitive way. The published data can be easily reviewed and maintained by the community, e.g. a group of collaborators.
This potential for sharing and building data made me decide to start using a Scratchpad. Hopefully, some of you will join me in this new way to participate in science.
See here, for more details on Scratchpads and what they are all about.
Functionality that I personally like are modules for bibliography, image galleries, phylogenetic trees, character matrices (under development), distribution maps. Also functionality is available for web fora and newsletters (both with email integration) and user blogs.
After an intensive day of training I have updated the Orthalicoidea site at several points. Have a look yourself!
Needless to say that this will always be a work in progress, evolving slowly, but hopefully steadily...
Reference:
Sarkar, I.N., 2009. Biodiversity Informatics: the emergence of a field. BMC Bioinformatics 10 (Suppl. 14): S1
News on old papers
15-12-2009 11:26
E-publication and SCI
20-10-2009 22:26
The International
Commission on Zoological Nomenclature is now
discussing the possibility of electronic-only
publications. Until now publication of a new name is
only valid if the paper is also printed on paper and
distributed to a number of institutions. The
Commission has recently published a number of comments on the
proposal to change the Code.
Electronic publication is usually interpreted as e-version of papers in journals. Some journals, like PLoS, only appear electronically and this quite rapidly followed by other journals. Even museums are progressing on this track, the journals of e.g. Naturalis will undoubtedly no longer be printed within a few years.
Another way of publishing electronically is putting data in databases, making these avaialble on the net, or in dedicated templates, e.g. Scratchpad, EOL, LifeDesk. In short: web-based taxonomy. This is potentially more useful on a longer term as the comprehensiveness is much bigger. Moreover it may be coupled to initiatives like Open Taxonomy, stimulating non-professional users to contribute in various ways.
With the on-going rat-race, it is the SCI that rules the universities and even natural history museums are getting influenced. Taxonomists are stimulated to perform “high profile research” (alpha-taxonomy being ‘sooo 20th century...’) and only publications in “high-ranking SCI journals” are being seen as useful. It may be the dilusion of the day, but this viral idea is spreading rapidly. While in some science departments journals are being trashed after 10 years, their contents being totally irrelevant, taxonomic publications will stay useful and remain so since 1758. Some ‘managers’ fail to grasp this fact and unless they manage to change the Code or make taxonomy obsolete in other ways, impact factors should be treated in a different way.
Recently, PLoS has introduced article-level metrics of usage. Although this might be considered as progress by some, I still wonder when contributions to (web-based) taxonomy will be fully valued. Without that, SCI-ranking in its current form has to be valued of little use for taxonomy. About SCI and the pitfalls of citation index, see also Reedijk & Moed (2008).
Reference:
Reedijk, J. & Moed, H.F., 2008. Is the impact of journal impact factors decreasing? - Journal of Documentation 64: 183-192.
Electronic publication is usually interpreted as e-version of papers in journals. Some journals, like PLoS, only appear electronically and this quite rapidly followed by other journals. Even museums are progressing on this track, the journals of e.g. Naturalis will undoubtedly no longer be printed within a few years.
Another way of publishing electronically is putting data in databases, making these avaialble on the net, or in dedicated templates, e.g. Scratchpad, EOL, LifeDesk. In short: web-based taxonomy. This is potentially more useful on a longer term as the comprehensiveness is much bigger. Moreover it may be coupled to initiatives like Open Taxonomy, stimulating non-professional users to contribute in various ways.
With the on-going rat-race, it is the SCI that rules the universities and even natural history museums are getting influenced. Taxonomists are stimulated to perform “high profile research” (alpha-taxonomy being ‘sooo 20th century...’) and only publications in “high-ranking SCI journals” are being seen as useful. It may be the dilusion of the day, but this viral idea is spreading rapidly. While in some science departments journals are being trashed after 10 years, their contents being totally irrelevant, taxonomic publications will stay useful and remain so since 1758. Some ‘managers’ fail to grasp this fact and unless they manage to change the Code or make taxonomy obsolete in other ways, impact factors should be treated in a different way.
Recently, PLoS has introduced article-level metrics of usage. Although this might be considered as progress by some, I still wonder when contributions to (web-based) taxonomy will be fully valued. Without that, SCI-ranking in its current form has to be valued of little use for taxonomy. About SCI and the pitfalls of citation index, see also Reedijk & Moed (2008).
Reference:
Reedijk, J. & Moed, H.F., 2008. Is the impact of journal impact factors decreasing? - Journal of Documentation 64: 183-192.
More publications
20-08-2009 12:46
A few more
papers
appeared in print yesterday, all in Dutch this time.
They are published in Spirula, a periodical of the
Dutch Malacological Society. However, two have
English summaries and those of you who regularly
follow this blog will recognize the topics.
The first paper is my laudatio for Dolf van Bruggen during the celebration of his 80th birthday. I take the opportunity to put up a picture here that was taken during that ceremony.
Dr. Dolf van Bruggen during his
closing word. On the right-hand side Dr. Hans
Kuiper, one of the other Honorary Members of the
Dutch Malacological Society (Photo: Ton de
Winter).
The second paper is on the putty eating snails that I mentioned in this post. And finally, there is a paper on my Suriname project.
The first paper is my laudatio for Dolf van Bruggen during the celebration of his 80th birthday. I take the opportunity to put up a picture here that was taken during that ceremony.
Dr. Dolf van Bruggen during his
closing word. On the right-hand side Dr. Hans
Kuiper, one of the other Honorary Members of the
Dutch Malacological Society (Photo: Ton de
Winter).The second paper is on the putty eating snails that I mentioned in this post. And finally, there is a paper on my Suriname project.
Publications available
18-08-2009 20:52
My
recent
publications
in the Festschrift for Dolf van Bruggen are now
available online at the journal’s
website.
Online publication (2)
01-06-2009 10:00
Today a paper was published which may possibly be
seen as a milestone in online publishing of taxonomic
works (Miller et al., 2009a). It is not about
Neotropical snails; it is not even about snails. It
is about Chinese spiders. Why then bother in this
blog?
While the future of taxonomy seems with online publication, there is much debate about it and more and more taxonomists have a preference for journals that are freely accessible (Penev et al., 2008). Until now, however, an example was lacking following a clear framework and tackling some of the remaininbg stumble-blocks (e.g. the poor quality of GBIF data). Penev et al. (2009) now propose the following scheme, which is used in the open access journal of ZooKeys.
Jeremy Miller, first author of the underlying taxonomic work, showed me last week already the datasets (Miller et al., 2009b, c) and how they worked. Especially the link with Google Earth is very nice, with data on the species showing up when the locality pin is clicked upon. A link to MorphBank is included, in which pictures of the species are stored.
This model provides a good methodology for online publication, while assuring at the same time that the data are of high quality and freely accessible.
References:
Miller J.A., Griswold C.E., Yin C.M. 2009a. The symphytognathoid spiders of the Gaoligongshan, Yunnan,
China (Araneae, Araneoidea): Systematics and diversity of micro-orbweavers. - ZooKeys 11: 9-195. doi: 10.3897/zoo-
keys.11.160
Miller J.A., Griswold C.E., Yin C.M. 2009b. Appendix B. Locality data (XLS format) for all specimens of the
spider families Th eridiosomatidae, Mysmenidae, Anapidae, and Symphytognathidae collected during an inventory of
the Gaoligongshan, Yunnan, China, 1998-2007. DATASET. File format: Microsoft Excel (1997-2003). doi: 10.3897/
zookeys.11.160-app.B.dt. - ZooKeys 11: 9-195. doi: 10.3897/zookeys.11.160
Miller J.A., Griswold C.E., Yin C.M., 2009c. Appendix C. Locality data (KML format) for all specimens of the
spider families Th eridiosomatidae, Mysmenidae, Anapidae, and Symphytognathidae collected during an inventory of
the Gaoligongshan, Yunnan, China, 1998-2007. DATASET. File format: KML (Keyhole Markup Language) version
2.1 for GoogleEarth. doi: 10.3897/zookeys.11.160-app.C.dt. - ZooKeys 11: 9-195. doi: 10.3897/zookeys.11.160
Penev L., Erwin T., Thompson F.C., Sues H-D., Engel M.S., Agosti D., Pyle R., Ivie M., Assmann
T., Henry T., Miller J., Ananjeva N.B., Casale A., Lourenco W., Golovatch S., Fagerholm H-P.,
Taiti S., Alonso-Zarazaga M., 2008. ZooKeys, unlocking Earth’s incredible biodiversity and
building a sustainable bridge into the public domain: From “print-based” to “web-based”
taxonomy, systematics, and natural history. ZooKeys Editorial Opening Paper. - ZooKeys 1:
1-7. doi: 10.3897/zookeys.1.11
Penev L., Erwin T., Miller J., Chavan V., Moritz T., Griswold C., 2009. Publication and dissemination of data-
sets in taxonomy: ZooKeys working example. ZooKeys 11: 1-8. doi: 10.3897/zookeys.11.210
While the future of taxonomy seems with online publication, there is much debate about it and more and more taxonomists have a preference for journals that are freely accessible (Penev et al., 2008). Until now, however, an example was lacking following a clear framework and tackling some of the remaininbg stumble-blocks (e.g. the poor quality of GBIF data). Penev et al. (2009) now propose the following scheme, which is used in the open access journal of ZooKeys.
Jeremy Miller, first author of the underlying taxonomic work, showed me last week already the datasets (Miller et al., 2009b, c) and how they worked. Especially the link with Google Earth is very nice, with data on the species showing up when the locality pin is clicked upon. A link to MorphBank is included, in which pictures of the species are stored.
This model provides a good methodology for online publication, while assuring at the same time that the data are of high quality and freely accessible.
References:
Miller J.A., Griswold C.E., Yin C.M. 2009a. The symphytognathoid spiders of the Gaoligongshan, Yunnan,
China (Araneae, Araneoidea): Systematics and diversity of micro-orbweavers. - ZooKeys 11: 9-195. doi: 10.3897/zoo-
keys.11.160
Miller J.A., Griswold C.E., Yin C.M. 2009b. Appendix B. Locality data (XLS format) for all specimens of the
spider families Th eridiosomatidae, Mysmenidae, Anapidae, and Symphytognathidae collected during an inventory of
the Gaoligongshan, Yunnan, China, 1998-2007. DATASET. File format: Microsoft Excel (1997-2003). doi: 10.3897/
zookeys.11.160-app.B.dt. - ZooKeys 11: 9-195. doi: 10.3897/zookeys.11.160
Miller J.A., Griswold C.E., Yin C.M., 2009c. Appendix C. Locality data (KML format) for all specimens of the
spider families Th eridiosomatidae, Mysmenidae, Anapidae, and Symphytognathidae collected during an inventory of
the Gaoligongshan, Yunnan, China, 1998-2007. DATASET. File format: KML (Keyhole Markup Language) version
2.1 for GoogleEarth. doi: 10.3897/zookeys.11.160-app.C.dt. - ZooKeys 11: 9-195. doi: 10.3897/zookeys.11.160
Penev L., Erwin T., Thompson F.C., Sues H-D., Engel M.S., Agosti D., Pyle R., Ivie M., Assmann
T., Henry T., Miller J., Ananjeva N.B., Casale A., Lourenco W., Golovatch S., Fagerholm H-P.,
Taiti S., Alonso-Zarazaga M., 2008. ZooKeys, unlocking Earth’s incredible biodiversity and
building a sustainable bridge into the public domain: From “print-based” to “web-based”
taxonomy, systematics, and natural history. ZooKeys Editorial Opening Paper. - ZooKeys 1:
1-7. doi: 10.3897/zookeys.1.11
Penev L., Erwin T., Miller J., Chavan V., Moritz T., Griswold C., 2009. Publication and dissemination of data-
sets in taxonomy: ZooKeys working example. ZooKeys 11: 1-8. doi: 10.3897/zookeys.11.210
Online publication
25-05-2009 14:48
There is some debate now on the
TaxCom mailing list
about the recent publication of Costello (2009). His
paper argues that biodiversity data should be
published online, but that “scientists’ concerns
about these efforts have not been answered and
initiatives to motivate scientists to comply have
been inadequate”.
It cannot be denied that online publication can be a powerful tool and there are several nice examples that could be mentioned. To name just a few that I have recently accessed: Gary Rosenberg’s site on Jamaican molluscs and the World Spiders Catalog, maintained by Norman Platnick. [No, I’m not switching from malacology to arachnology...]. These are sites made and maintained by individual specialists; besides these selective exemples, many more could be cited. My impression is that quality is excellent to good and possibly the main caveat is that, after a while and for whatever reason, the site is no longer updated.
The other extreme are sites (or rather portals) than host a huge amount of data and make these available for further use. A well-known example is the Global Biodiversity Information Facility (GBIF). Unfortunately, it is also this example that shows the pitfalls of these data centers. As far as my specialism is concerned, the data is notoriously unreliable. It is also outrageously incomplete. And that’s one of the main points of Costello’s critique: many primary data, which were gathered using public funds, are not available through data centers for further research and several other benefits that are listed in his paper.
His proposal is to drastically alter the way scientists publish their data, moving them from print to online data centers.
There are several useful suggestions made in his paper to motivate people for online publication, e.g. to stimulate the use of giving credit to authors who upload data, to facilitate the use of tools (such as Scratchpads) and requirements by funding agencies.
The advantages of online publication are clear. However, I feel that we still have a long way to go. To name a few of the remaining stumble blocks: quality checking, involvement of scientific amateurs (who also generate primary data) and to re-think the business model that sustains now many societies that issue scientific journals. Not all publications are commercial and hence publishing data as such can have adverse effects which have not been mentioned so far.
I know, there is much more that can be said about this topic...
Reference:
Costello, M., 2009. Motivating online publication of data. BioScience 59: 418-427.
It cannot be denied that online publication can be a powerful tool and there are several nice examples that could be mentioned. To name just a few that I have recently accessed: Gary Rosenberg’s site on Jamaican molluscs and the World Spiders Catalog, maintained by Norman Platnick. [No, I’m not switching from malacology to arachnology...]. These are sites made and maintained by individual specialists; besides these selective exemples, many more could be cited. My impression is that quality is excellent to good and possibly the main caveat is that, after a while and for whatever reason, the site is no longer updated.
The other extreme are sites (or rather portals) than host a huge amount of data and make these available for further use. A well-known example is the Global Biodiversity Information Facility (GBIF). Unfortunately, it is also this example that shows the pitfalls of these data centers. As far as my specialism is concerned, the data is notoriously unreliable. It is also outrageously incomplete. And that’s one of the main points of Costello’s critique: many primary data, which were gathered using public funds, are not available through data centers for further research and several other benefits that are listed in his paper.
His proposal is to drastically alter the way scientists publish their data, moving them from print to online data centers.
There are several useful suggestions made in his paper to motivate people for online publication, e.g. to stimulate the use of giving credit to authors who upload data, to facilitate the use of tools (such as Scratchpads) and requirements by funding agencies.
The advantages of online publication are clear. However, I feel that we still have a long way to go. To name a few of the remaining stumble blocks: quality checking, involvement of scientific amateurs (who also generate primary data) and to re-think the business model that sustains now many societies that issue scientific journals. Not all publications are commercial and hence publishing data as such can have adverse effects which have not been mentioned so far.
I know, there is much more that can be said about this topic...
Reference:
Costello, M., 2009. Motivating online publication of data. BioScience 59: 418-427.
A new book announced
05-05-2009 21:39
Books on Neotropical snails are scarce and additions
are very welcome. Modesto Correoso send me notice
that - after a long production process - his book on
non-marine snails of continental Ecuador has recently
been published.
Awaiting further details on this new addition to the malacological library, I’ll keep you posted once the copy ordered arrives on my desk.
Update:
Here is a picture of the formal presentation of the book (the author at left).
Awaiting further details on this new addition to the malacological library, I’ll keep you posted once the copy ordered arrives on my desk.
Update:
Here is a picture of the formal presentation of the book (the author at left).
A new paper
06-04-2009 17:37
Today my paper on a revision of the Orthalicidae from
Venezuelan Guayana was published in
Zootaxa.
Later this week more on it.
Later this week more on it.
Taking pictures is a craft
29-11-2008 12:34
Needing several pictures to illustrate an upcoming
paper, I finally had the opportunity to make some
photographs at Naturalis. While at previous occasions
this was done at a photography room with expert
assistance of a colleague, this time it was a
provisional set-up and I was on my own.
Quickly I discovered that taking shell pictures is a real craft. You can switch on the automatic mode, but it won’t help very much. Not only the different components of the set-up have to be geared towards the object (the shell), some practical tricks appeared necessary. A difficult (because very shining) shell shows the results.
On the first picture I used a ring of TL light, which eliminated shadows but produced too much of a white ‘blob’. When I switched lights, the colour of the shell became too unnatural and I had to adapt the white balance to obtain the natural colours of the shell (picture 2-5).
Because this shell was so shining I was still not satisfied with the result and experimented with dimming the light by placing a white sheet of paper between the lamp and the shell. Picture 6 shows how the improvement looks after one side, leaving a dark shadow around the top and too much reflection at the bottom of the shell.
The result is now quite reasonable, but one final step appears to be necessary. Because it was a stand-alone set-up without connection between the camera and computer, I was unable to immediately judge the results. They looked good on the screen, but after transferral of the pictures to the computer, it was clear that one extra round is needed to improve the depth of field...
Science is not only observation, thinking and writing, but also overcoming a lot of practical hurdles.
Quickly I discovered that taking shell pictures is a real craft. You can switch on the automatic mode, but it won’t help very much. Not only the different components of the set-up have to be geared towards the object (the shell), some practical tricks appeared necessary. A difficult (because very shining) shell shows the results.
On the first picture I used a ring of TL light, which eliminated shadows but produced too much of a white ‘blob’. When I switched lights, the colour of the shell became too unnatural and I had to adapt the white balance to obtain the natural colours of the shell (picture 2-5).
Because this shell was so shining I was still not satisfied with the result and experimented with dimming the light by placing a white sheet of paper between the lamp and the shell. Picture 6 shows how the improvement looks after one side, leaving a dark shadow around the top and too much reflection at the bottom of the shell.
The result is now quite reasonable, but one final step appears to be necessary. Because it was a stand-alone set-up without connection between the camera and computer, I was unable to immediately judge the results. They looked good on the screen, but after transferral of the pictures to the computer, it was clear that one extra round is needed to improve the depth of field...
Science is not only observation, thinking and writing, but also overcoming a lot of practical hurdles.
I have a dream...
24-10-2008 07:34
The European malacofauna is well known, although
still from time to time some cryptic new species are
discovered or new faunal elements reported. But
still, for a Palaearctic malacologist taxonomy is not
the most exciting field. Still there remains enough
to do, e.g. compiling faunal overviews.
The Dutch Malacological Society recently had the initiative to publish very practical overviews that even can be carried into the field for rapid identification of snails. These so called ‘search cards’ cover the whole malacofauna of the Netherlands: marine, freshwater and land snails. They have been adapted from a similar issue for Germany. I depict only the land version, issued on a two-sided plastic coated A4-sheet. There has been substantial media coverage, e.g. here (link to TV programme ‘Vroege Vogels’ 21.10.2008)
More information on the NMV website
Now you may ask: what is my dream?
One day, I hope, there will be similar issues for Neotropical countries. Perhaps in adapted form to allow for the multitude of species (less than 200 species in Holland), but still suitable for the general public. Perhaps a field book or a poster or any other educational form that brings malacology to the attention of children and adults. Besides, if you don’t know what is in your fauna, you will never be motivated to protect it. And there is much more than those attractive mammals or those beautiful birds!
For some regions the basic material is already available, e.g. the recent checklist for Central America and the book of Simone for Brazil. Perhaps a topic to be discussed on the next CLAMA meeting?
The Dutch Malacological Society recently had the initiative to publish very practical overviews that even can be carried into the field for rapid identification of snails. These so called ‘search cards’ cover the whole malacofauna of the Netherlands: marine, freshwater and land snails. They have been adapted from a similar issue for Germany. I depict only the land version, issued on a two-sided plastic coated A4-sheet. There has been substantial media coverage, e.g. here (link to TV programme ‘Vroege Vogels’ 21.10.2008)
More information on the NMV website
Now you may ask: what is my dream?
One day, I hope, there will be similar issues for Neotropical countries. Perhaps in adapted form to allow for the multitude of species (less than 200 species in Holland), but still suitable for the general public. Perhaps a field book or a poster or any other educational form that brings malacology to the attention of children and adults. Besides, if you don’t know what is in your fauna, you will never be motivated to protect it. And there is much more than those attractive mammals or those beautiful birds!
For some regions the basic material is already available, e.g. the recent checklist for Central America and the book of Simone for Brazil. Perhaps a topic to be discussed on the next CLAMA meeting?
Priority = time, but place matters
21-10-2008 08:41
The rule is simple. He who publishes a taxon first
has priority with his name (provided that the
ICZN-rules are followed). This rule can effect the
choice of the outlet. There is a vast array of
journals, often with their own target groups, but
only a limited number of them will publish taxonomic
works. One could expect a ‘natural selection’ towards
the more well-known, international journals.
Especially since many scientists are longing to have
their papers published in ISI-rated journals (the
dream of many taxonomists is to have once a paper in
Nature or Science, few are lucky enough to reach
their goal). However, there are always exceptions for
whatever reasons. But even then the importance of the
outlet can matter. An (non-Neotropical) example may
illustrate this.
In 2006 Christian Altaba described a fossil helicodontid from Mallorca as Darderia bellverica, and submitted his paper to a journal which was published early 2007. The same taxon has been described as Oestophora cuerdai by Quintana, Vicens & Pons, 2007. The result was a discussion about the publication date*, largely due to the fact that both journals were published later than the year in which the volume was due. This highlights the role of the editor and his sense for precision, viz. to clearly and correctly state the actual date of publication on the cover. High-standards journals are then clearly in advantage. But ultimately it is the author who chooses in which journal he wants to publish his paper. Especially when describing new taxa, this example tells us how the place can matter.
References:
Altaba, C.R., 2006 [2007]. A new land snail from the Quartenary of Mallora (Belearic Islands, Western Medeiterranean): Darderia bellverica n.gen n.sp. (Gastropoda, Pulmonata, Helicondontidae). - Anim. Biod. Cons. 29: 195-200.
*Altaba, C.R., 2007. Reply to Quintana et al. (2007): Darderia bellverica Altaba, 2007 is the correct name for the Mallorcan fossil helicondontid. - Spira 2: 191-196.
Quintana, J., Vicens, D. & Pons, G.X., 2006 [2007]. A new species of the genus Oestrophora Hesse, 1907 (Gastropoda: Pulmonata: Trissexodontidae) from the Upper Pleistocene of Mallorca (Belearic Islands, Western Mediterranean). - Bol. Soc. Hist. Nat. Bal. 49: 51-58.
*Quintana, J., Pons, G.X. & Vicens, D., 2007. Algunas anotaciones criticas sobre Oestrophora cuerdai Quintana, Vicens et Pons, 2006 (Mollusca: Pulmonata: Helicodontidae). - Spira 2: 157-162.
Update:
Christian Altaba (pers. comm.) suggested that ZooBank could solve this kind of situations once it is fully operational. I think he is right.
In 2006 Christian Altaba described a fossil helicodontid from Mallorca as Darderia bellverica, and submitted his paper to a journal which was published early 2007. The same taxon has been described as Oestophora cuerdai by Quintana, Vicens & Pons, 2007. The result was a discussion about the publication date*, largely due to the fact that both journals were published later than the year in which the volume was due. This highlights the role of the editor and his sense for precision, viz. to clearly and correctly state the actual date of publication on the cover. High-standards journals are then clearly in advantage. But ultimately it is the author who chooses in which journal he wants to publish his paper. Especially when describing new taxa, this example tells us how the place can matter.
References:
Altaba, C.R., 2006 [2007]. A new land snail from the Quartenary of Mallora (Belearic Islands, Western Medeiterranean): Darderia bellverica n.gen n.sp. (Gastropoda, Pulmonata, Helicondontidae). - Anim. Biod. Cons. 29: 195-200.
*Altaba, C.R., 2007. Reply to Quintana et al. (2007): Darderia bellverica Altaba, 2007 is the correct name for the Mallorcan fossil helicondontid. - Spira 2: 191-196.
Quintana, J., Vicens, D. & Pons, G.X., 2006 [2007]. A new species of the genus Oestrophora Hesse, 1907 (Gastropoda: Pulmonata: Trissexodontidae) from the Upper Pleistocene of Mallorca (Belearic Islands, Western Mediterranean). - Bol. Soc. Hist. Nat. Bal. 49: 51-58.
*Quintana, J., Pons, G.X. & Vicens, D., 2007. Algunas anotaciones criticas sobre Oestrophora cuerdai Quintana, Vicens et Pons, 2006 (Mollusca: Pulmonata: Helicodontidae). - Spira 2: 157-162.
Update:
Christian Altaba (pers. comm.) suggested that ZooBank could solve this kind of situations once it is fully operational. I think he is right.
Beauty is in the eye of the beholder
29-07-2008 13:27
Dissecting and illustrating a snail may not be as
easy as it seems, especially if you haven't practiced
it anymore for so many years :-)
However, after a long day in the lab I managed to produce this drawing:
It is reasonably nice, but perhaps not more than just that. Compare it e.g. to the illustrations that my friend Jaap Vermeulen uses for his papers, like this one:
Lesson for this day: illustrating is a profession. But beauty is in the eye of the beholder...
However, after a long day in the lab I managed to produce this drawing:
It is reasonably nice, but perhaps not more than just that. Compare it e.g. to the illustrations that my friend Jaap Vermeulen uses for his papers, like this one:
Lesson for this day: illustrating is a profession. But beauty is in the eye of the beholder...
Accepted!
03-04-2008 15:23
Today my paper on Ecuador was accepted :-))
Although it has taken a while (submitted 19 November 2007, revised version 19 February), it was a very instructive experience. After all, it is more than 20 years ago that my last scientific paper was published. One thing is for sure, the editing process demands now a lot more of authors than it used to be...
You can find more details on the paper under 'New Granada'. Some figures that partially will go with it are below, illustrating the localities and the main results.
Although it has taken a while (submitted 19 November 2007, revised version 19 February), it was a very instructive experience. After all, it is more than 20 years ago that my last scientific paper was published. One thing is for sure, the editing process demands now a lot more of authors than it used to be...
You can find more details on the paper under 'New Granada'. Some figures that partially will go with it are below, illustrating the localities and the main results.
Going through some rapids
25-11-2007 22:01
While sometimes things
just proceed slowly and steadily, this weekend felt
like steering a canoe through the rapids. But in a
pleasant way...
I submitted my publication to Zootaxa, only some minor technicalities need to be fixed before the review process will start. That is an exciting feeling, after so many years of not being able to publish!
One of the things I decided to give priority, was to revise and edit the Orthalicoidea from Francisco Borrero's checklist for Colombia. Many minor mistakes were corrected, but it is certainly a great advantage to have such a solid basis to work on, instead of having to collect all the data one by one. I made good progress and showed some pages to Francisco, who approved the idea for a joint paper.
He also mentioned that he has contacts with Fundación Jocotoco, an organisation that manages eight nature reserves in Ecuador. Plans are being made to set up a cooperation with the Cincinnati Museum and to start joint field work in the reserves. This could open up exciting new prospects...
Finally, out of the blue, I received today an email from someone in Perú, seeking identification of some Bulimulidae. I was able to quickly give him my opinion on the species figured (he had made excellent pictures!) and within short I received photos of some other unidentified species. As such people with an apparent keen interest in land snails are quite rare, I offered him help with literature since many old books and journals are difficult to consult in South America. And this way the contact network with like-minded people grows, slowly but steadily...
I submitted my publication to Zootaxa, only some minor technicalities need to be fixed before the review process will start. That is an exciting feeling, after so many years of not being able to publish!
One of the things I decided to give priority, was to revise and edit the Orthalicoidea from Francisco Borrero's checklist for Colombia. Many minor mistakes were corrected, but it is certainly a great advantage to have such a solid basis to work on, instead of having to collect all the data one by one. I made good progress and showed some pages to Francisco, who approved the idea for a joint paper.
He also mentioned that he has contacts with Fundación Jocotoco, an organisation that manages eight nature reserves in Ecuador. Plans are being made to set up a cooperation with the Cincinnati Museum and to start joint field work in the reserves. This could open up exciting new prospects...
Finally, out of the blue, I received today an email from someone in Perú, seeking identification of some Bulimulidae. I was able to quickly give him my opinion on the species figured (he had made excellent pictures!) and within short I received photos of some other unidentified species. As such people with an apparent keen interest in land snails are quite rare, I offered him help with literature since many old books and journals are difficult to consult in South America. And this way the contact network with like-minded people grows, slowly but steadily...
Version 0.2 is up
09-09-2007 21:26
The checklist of
Orthalicidae from Ecuador is taking shape. I have
checked now the following collections: ANSP
(Philadelphia), FMNH (Chicago), FLMNH (Gainesville),
RMNH (Leiden) and USNM (Washington). There remain a
number to be done, but as far as I can guess the
number of taxa is quite complete. So after some
polishing I have put up version 0.2 on the web. Its
main changes are:
- Orthalicinae added (checked with Strebel, 1909);
- the longitude/latitude coordinates of the localities have been centralized in Table 1, to improve the readableness of the text;
- the taxa have been numbered;
- a start has been made with some analyses.
This week I also made progress with the inventory of type material in the Naturalis collection. Some 170 have been listed so far, of which 15 manuscript names, mostly of Weyrauch (another project coming up).
- Orthalicinae added (checked with Strebel, 1909);
- the longitude/latitude coordinates of the localities have been centralized in Table 1, to improve the readableness of the text;
- the taxa have been numbered;
- a start has been made with some analyses.
This week I also made progress with the inventory of type material in the Naturalis collection. Some 170 have been listed so far, of which 15 manuscript names, mostly of Weyrauch (another project coming up).