September 2016 - DFFU_IAS - lists.gbif.org

Re: [DFFU_IAS] time from observation to publication on GBIF
by Quentin Groom 26 Sep '16

26 Sep '16

Hi Tim, thanks that's all useful information. You confirmed what I suspected regarding the dates of publication. As I was working with the data I noticed several problems and biases that confuse the results. A subset of 100 species is really too small to start breaking down into different subsets. As you noted the over representation of birds Perhaps, the only take home message we should make at the moment is that publishing of these data is not fast and that it would need to be improved if GBIF were used for early warning. I would not make any conclusions about the improvement in speed of publication. This is an small and biased subset. Regards Quentin Dr. Quentin Groom (Botany and Information Technology) Botanic Garden Meise Domein van Bouchout B-1860 Meise Belgium ORCID: 0000-0002-0596-5376 <http://orcid.org/0000-0002-0596-5376> Landline; +32 (0) 226 009 20 ext. 364 FAX: +32 (0) 226 009 45 E-mail: quentin.groom(a)plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.be On 26 September 2016 at 09:34, Tim Robertson <trobertson(a)gbif.org> wrote: > Hi Quentin, > *[I am not sure this message will be delivered to the TG as it is a closed > group – please consider forwarding it on if you think it is worthwhile]* > > It’s great to see these charts and a little saddening at the same time > that things aren’t speeding up. > > I’d just like to make sure you are aware of a possible issue in your > analysis. You may already have safeguarded against this but I raise it > just in case. It might be insignificant since you are dealing with a small > group of species but under certain circumstances could introduce a large > inaccuracy and should be verified. > > At GBIF.org we repeatedly index datasets. You are probably aware that > data management practice varies wildly across institutions, and it is a > common thing that people delete a dataset and republish it e.g. 1. moving > from DiGIR to IPT without following recommended guidelines or 2. changing > record identifiers for the same original record - all UK NBN data have done > this over the years. When this happens, the original individual records > are deleted, and new ones created receiving a new created_date but the > event date will remain the same. The result is you'd get a larger lag than > was the reality. > > The only feasibly way I can see to safeguard against this would be to > analyse the the gbif ID over the snapshots and identify cases where > records are then deleted and recreated (perhaps considering combination of > location,species,date?). I have raised this with groups doing this kind of > study before but to my knowledge it’s been ignored. > > Just for ideas: > It might be worthwhile considering individual datasets and the publishing > protocol. I strongly suspect that a very few datasets could be recognised > as key conduits for this kind of data – e.g. iNaturalist and Artdatabankem > (Sweden) would presumably be less than 1 week and I suspect IPTs might be > faster - similar to observation data versus specimen. The publishing > country might be interesting too and whether there are few who are clearly > more active than others. That would be an interesting metric on countries > in general of course. Then there is eBird, which is a huge dataset and will > skew results for birds heavily because it is an annual publication with an > inherent lag of around 0.5 – 1.5 years. > > I know all too well that as soon as you’ve shared some metrics, you > immediately get a ton more work to do – I hope this is useful information > though. > > Many thanks, > Tim > > > From: Quentin Groom <quentin.groom(a)plantentuinmeise.be> > Date: Sunday 25 September 2016 at 13:53 > To: Task Group on Data Fitness for Use in Research on Invasive Alien > Species <dffu_ias(a)lists.gbif.org>, Tim Robertson <trobertson(a)gbif.org>, > Jan Legind <jlegind(a)gbif.org> > Subject: Re: time from observation to publication on GBIF > > One further graph... > > These observations are separated into the main classes. Clearly birds are > by far the most common observation, note the logarithmic scale. The data > hints that the publication rate for mammals is slower, but it is not clear. > Regards > Quentin > > [image: Inline images 1] > > > > > > Dr. Quentin Groom > (Botany and Information Technology) > > Botanic Garden Meise > Domein van Bouchout > B-1860 Meise > Belgium > > ORCID: 0000-0002-0596-5376 <http://orcid.org/0000-0002-0596-5376> > > Landline; +32 (0) 226 009 20 ext. 364 > FAX: +32 (0) 226 009 45 > > E-mail: quentin.groom(a)plantentuinmeise.be > Skype name: qgroom > Website: www.botanicgarden.be > > > On 25 September 2016 at 13:19, Quentin Groom <quentin.groom@ > plantentuinmeise.be> wrote: > >> I've had a look at the GBIF data for the 100 Worst Aliens. Just to remind >> you, the intention is to see how long it takes for the records of invasive >> species take to reach GBIF. >> >> This first graph is a histogram showing the days between observation >> (eventdate) and publication date (date_created) for each publication year. >> What is notable is that there is no indication that the time to publication >> is reducing with time. The GBIF analytics suggest that data are getting to >> GBIF faster, but this is not clear from this subset ( >> http://www.gbif.org/analytics/global). >> >> [image: Inline images 4] >> >> Grouping all the observations together this histogram summarises the rate >> of publication. Clearly, most observations take longer than a year to be >> published. >> [image: Inline images 2] >> >> This is the same as above except for specimens. The numbers of records >> are a lot less and I assume they take longer to get to GBIF as a result of >> the the current digitisation of herbaria and museums. >> [image: Inline images 3] >> >> Regards >> Quentin >> >> >> Dr. Quentin Groom >> (Botany and Information Technology) >> >> Botanic Garden Meise >> Domein van Bouchout >> B-1860 Meise >> Belgium >> >> ORCID: 0000-0002-0596-5376 <http://orcid.org/0000-0002-0596-5376> >> >> Landline; +32 (0) 226 009 20 ext. 364 >> FAX: +32 (0) 226 009 45 >> >> E-mail: quentin.groom(a)plantentuinmeise.be >> Skype name: qgroom >> Website: www.botanicgarden.be >> >> >

2 1

time from observation to publication on GBIF
by Quentin Groom 25 Sep '16

25 Sep '16

I've had a look at the GBIF data for the 100 Worst Aliens. Just to remind you, the intention is to see how long it takes for the records of invasive species take to reach GBIF. This first graph is a histogram showing the days between observation (eventdate) and publication date (date_created) for each publication year. What is notable is that there is no indication that the time to publication is reducing with time. The GBIF analytics suggest that data are getting to GBIF faster, but this is not clear from this subset ( http://www.gbif.org/analytics/global). [image: Inline images 4] Grouping all the observations together this histogram summarises the rate of publication. Clearly, most observations take longer than a year to be published. [image: Inline images 2] This is the same as above except for specimens. The numbers of records are a lot less and I assume they take longer to get to GBIF as a result of the the current digitisation of herbaria and museums. [image: Inline images 3] Regards Quentin Dr. Quentin Groom (Botany and Information Technology) Botanic Garden Meise Domein van Bouchout B-1860 Meise Belgium ORCID: 0000-0002-0596-5376 <http://orcid.org/0000-0002-0596-5376> Landline; +32 (0) 226 009 20 ext. 364 FAX: +32 (0) 226 009 45 E-mail: quentin.groom(a)plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.be

1 1

IAS references at GBIF
by Dmitry Schigel 21 Sep '16

21 Sep '16

Hello group, As agreed, I will prepare a list of suggested literature extracting the list from the survey (when closed, we now have 191 answers, last reminder on 28 Sep) for you and someone here will check the refs against our current collection. This is to remind you that we do have a Mendeley library of the GBIF-tracked literature. Currently we have 353 papers tagged "invasives", 456 with search hits for "invasive" and 154 with hits for "alien", some of the papers are based on GBIF published data. This is not on the task list, and maybe there is not much time left for this, but just to let you know that it might be useful for you to do some sort of screening of the past studies (methods? criticism?), one may think that these papers are a survey in itself - but of real data uses, not only the needs claimed in the survey. There are a couple of ways you can access and explore the GBIF collection of IAS papers. 1. You install & open Mendeley desktop [1] (I very much prefer desktop over web version) and open GBIF public library there [2]. Using tags such as "invasives" or searching for "invasiv" etc. you would be able to narrow 3000+ reference to a useable subset of a several tens. 2. I can export those subsets and e-mail for you, the export formats are .bib, .ris and .xml (EndNote friendly). The example of the latter if opened in Excel is attached. 3. In any case, 1 or 2, you can use your institutional access to full text versions. After the group is dismissed you might like to use the outcome for some sort of review paper on data use in IAS? [1] https://www.mendeley.com/download-mendeley-desktop/ [2] http://www.mendeley.com/groups/1068301/gbif-public-library/ Dmitry

2 1

Skype follow up
by Melodie McGeoch 20 Sep '16

20 Sep '16

Greetings all Thank you for the constructive discussion via skype yesterday. I have updated the 'Tasks' document (link below) based on our discussion. As soon as Dmitry and I have discussed this with Varos and Greg and we have their input, I will merge the 2 tables, collate the points and include an agenda for the Melbourne meeting. Please take a look and comment/edit as necessary *Tasks from Leipzig to Melbourne_Revised Sept* https://drive.google.com/open?id=1cdtg5U9hEtiSlu9PVL0oAJoEEXWnwjfxZseD4byR4… All the best Melodie -- Melodie A. McGeoch Associate Professor, School of Biological Sciences, Monash University, Clayton Campus (Bld 18, Innovation Walk, Rm 121), Melbourne, Victoria 3800, Australia. Tel: +61 3 99020464, Mobile: +61 (0) 499 954180, E-mail: melodie.mcgeoch(a)monash.edu, ISI Researcher ID F-8353-2011, Research Group website: http://melodiemcgeoch.com/ *ORCID *http://orcid.org/0000-0003-3388-2241

1 0

Re: [DFFU_IAS] Reminder and agenda: Skype call on Monday
by Dmitry Schigel 19 Sep '16

19 Sep '16

Hello group, Please remember the Skype call in 1.5 hours. Dmitry From: Dmitry Schigel Sent: 16 September 2016 15:20 To: Task Group on Data Fitness for Use in Research on Invasive Alien Species Subject: Reminder and agenda: Skype call on Monday Hello group, Here is a reminder that we will have a Skype call on Monday, 19 Sep at 7:00 PM - 9:00 PM (Time zone: Eastern Time (Melbourne)) Check your time here: http://www.timeanddate.com/worldclock/meetingdetails.html?year=2016&month=9… I have now tidied up the draft agenda and added key links, including some homework: https://docs.google.com/document/d/1XYQ3epgurvjSEehYopmx_H0z-jANT0Qgn7RAn8g…<https://docs.google.com/document/d/1XYQ3epgurvjSEehYopmx_H0z-jANT0Qgn7RAn8g…> Feel free to add topics, links and other content. Best regards, Dmitry Schigel, PhD Programme Officer for Content Analysis and Use Global Biodiversity Information Facility (GBIF) Secretariat Universitetsparken 15 DK-2100 Copenhagen Ø DENMARK Office +45 35 32 14 85 Mobile +45 30 45 02 25 E-mail dschigel(a)gbif.org<mailto:dschigel@gbif.org> Web www.gbif.org<http://www.gbif.org/> [GBIFlogoNO_TEXT_50%]

2 1

FW: New GBIF Darwin Core Spreadsheet Templates
by Dmitry Schigel 19 Sep '16

19 Sep '16

Hello, Here comes the templates consultation I told you about, closing 21 September WED. Dmitry From: Siro Masinde Sent: 06 September 2016 10:22 To: nodes_IG(a)cemail.gbif.org Cc: Kyle Braak Subject: New GBIF Darwin Core Spreadsheet Templates Dear colleagues, Many GBIF data publishers without a database system nor the necessary expertise and resources to run an advanced data publishing infrastructure have frequently expressed the need for a simple template for capturing and formatting data for publication to GBIF. The previous tools to satisfy this need, the Darwin Core Spreadsheet Templates and Spreadsheet Processor, have not been kept up-to-date for a considerable time due to a range of challenges. The good news is that we have developed new GBIF data publishing templates. GBIF data publishing templates are a set of pre-configured Microsoft Excel spreadsheet files that serve as templates for capturing simple species checklists, occurrence data and sampling event data. The spreadsheets can be uploaded to the Integrated Publishing Toolkit (IPT). By using Darwin Core (DwC) term column headers, the IPT is able to automap the columns from the templates. Each template provides inline help and instructions in the worksheets. Currently the new Templates provide a simple solution for capturing and formatting three types of GBIF data classes, namely, Checklist Data, Occurrence Data and Sampling Event Data. Please check the following links to see the templates and feel free to try them as they are now - there'll be some minor adjustments before we launch them more widely but we'd appreciate your feedback. Checklist Data - https://github.com/gbif/ipt/wiki/checklistData#templates Occurrence Data - https://github.com/gbif/ipt/wiki/occurrenceData#templates Sampling Event Data - https://github.com/gbif/ipt/wiki/samplingEventData#templates In the light of these developments, we plan to decommission the old GBIF Darwin Core Spreadsheet Templates and Spreadsheet Processor and launch the new Templates by 21 September 2016. Should you have any concerns, observations or suggestions about these developments, please let us know at your earliest convenience. We shall very much appreciate it if you could pass on this information to potential users of the templates. Best regards, Kyle and Siro ------------------------------------------------------------------------------------------- Dr Siro Masinde Programme Officer for Content Mobilisation Global Biodiversity Information Facility (GBIF) Secretariat Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark Email: smasinde(a)gbif.org<mailto:smasinde@gbif.org> Skype: siro.masinde Tel: +45 3532 1477 Mob: +45 30450207 Fax: +45 2875 1480 Website: www.gbif.org<http://www.gbif.org/> -------------------------------------------------------------------------------------------

1 0

biocontrol catalogue
by Wilson, John <jrwilson＠sun.ac.za> 19 Sep '16

19 Sep '16

http://www.ibiocontrol.org/catalog/ The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer

1 0

table 1 and 2
by Dmitry Schigel 19 Sep '16

19 Sep '16

https://docs.google.com/document/d/1DaaT70IlW6sh0ARt4oUpHVsrU1zdbF6ic9czRru…

1 0

[DFFU_IAS] https://docs.google.com/document/d/1XYQ3epgurvjSEehYopmx_H0z-jANT0Qgn7RAn8gE58w/edit#
by Dmitry Schigel 19 Sep '16

19 Sep '16

https://docs.google.com/document/d/1XYQ3epgurvjSEehYopmx_H0z-jANT0Qgn7RAn8g…

1 0

Reminder and agenda: Skype call on Monday
by Dmitry Schigel 16 Sep '16

16 Sep '16

Hello group, Here is a reminder that we will have a Skype call on Monday, 19 Sep at 7:00 PM - 9:00 PM (Time zone: Eastern Time (Melbourne)) Check your time here: http://www.timeanddate.com/worldclock/meetingdetails.html?year=2016&month=9… I have now tidied up the draft agenda and added key links, including some homework: https://docs.google.com/document/d/1XYQ3epgurvjSEehYopmx_H0z-jANT0Qgn7RAn8g… Feel free to add topics, links and other content. Best regards, Dmitry Schigel, PhD Programme Officer for Content Analysis and Use Global Biodiversity Information Facility (GBIF) Secretariat Universitetsparken 15 DK-2100 Copenhagen Ø DENMARK Office +45 35 32 14 85 Mobile +45 30 45 02 25 E-mail dschigel(a)gbif.org Web www.gbif.org<http://www.gbif.org/> [GBIFlogoNO_TEXT_50%]

1 0