Date   

BONSAI & ARIES #communication

 

Dear BONSAI-Samurais,

I just sent out invitations for the k.LAB tour on Tuesday. Unfortunately, there will be no recording as no one seems to have the right software. Let's see it as a motivation to listen closely ;)

Those who have not received an invitation may hit me up via email (benjamin.portner@...) or simply use this button to join on the day of the meeting:

ARIES & BONSAI: k.LAB tour, Tuesday 1 December 2020, 17:00-18:30 CET

Join meeting



Also, please do not forget that there is a second meeting on Thursday, 3 December 2020, 17:00-18:30 CET to discuss opportunities for collaboration. Again, please get in touch if you have not received an invitation and would like to join - or use this button:

ARIES & BONSAI: opportunities for collaboration, Thursday 3 December 2020, 17:00-18:30 CET

 

Join meeting



Thank you and see y'all on Tuesday/Thursday!
Ben


Re: BONSAI Updates #meetingminutes #communication

 

Dear BONSAI-Samurais again,

It is decided! We shall meet ARIES on Thursday, 3 December 2020, 17:00-18:30 CET. I sent out invitations to those who participated in the poll. If you have not received an invitation and would like to join, please PM me your email address.

For the k.LAB-Tour, Ken would prefer Tuesday 1 December 2020, 17:00-18:30 CET. Those who would like to participate, please block this time frame. Instead of sending out invitations I have a request: I would like to record the tour so that all BONSAI members can look at it at a later time. Unfortunately, my organization's meeting tool does not support recordings. Does anyone here have access to a corresponding tool and can set up the meeting?

Cheers.
Ben


Re: BONSAI Updates #meetingminutes #communication

 

Dear BONSAI-Samurais,

thank you to those who have already participated in the poll to find a date for an exchange with ARIES. So far it looks like we have a majority for 3 December 2020 17:00-18:30 CET so please do not plan anything else for that date and time. I will leave the poll open one more week (until 20 November). Please inform those members who might be interested and have not voted yet.

All the best.
Ben


Re: Where can I find (or make) turtle files? #dataliberation

 

(moving this back to the original thread, apologies for posting to the wrong one before)

Thanks for your answers, Matteo and Søren! I was indeed talking about a machine accessible from anywhere, including but not limited to AAU. Such a machine might be useful for inspecting and manipulating exiobase in general, not just for converting it to an ontology. For now I am fine doing stuff on my laptop but things take long sometimes. Hence my curiosity.

Cheers.
Ben


-------------------------------------
From: Matteo

Currently the endpoint is running on a VM at AAU.
(which is quite hard to reach since you need two different steps VPN+proxy machine access)

I think Benjamin is talking about machine independent from AAU.

Also, it is important to note that the requirements (which are not so large by todays standards -- Thanks Moore!) are just if you plan to convert the entire Exiobase.

If you plan to work on YSTAFDB you can do it with your laptop.



---
Matteo Lissandrini

Department of Computer Science
Aalborg University

http://people.cs.aau.dk/~matteo






________________________________________

From: main@bonsai.groups.io <main@bonsai.groups.io> on behalf of Søren via groups.io <loekke@...>
Sent: 23 October 2020 14:52:18
To: main@bonsai.groups.io
Subject: Re: [bonsai] BONSAI Updates #communication #meetingminutes

In principle we should have a VM at AAU (funded by the ODA-project), but I do not know if it accessible and set up in a way that makes this possible(?) Maybe Matteo knows?

--------------------------------------------------
Ben:
Holy moly! The hardware requirements are intense. Do we have something like a central BONSAI cluster where we can run such code?


Re: BONSAI Updates #meetingminutes #communication

 

Dear BONSAI-Samurais!

I am back from my holiday and there is news from ARIES. They asked me to move both our meetings, the k.LAB software tour and the scoping of collaboration opportunities, to December. In response, I opened a new doodle poll. To keep the amount of double work small I suggest that we use this poll to determine both dates: The date with most votes will be reserved for the scoping, the date with second most votes will be reserved for the software tour. Please let me know if you are against this procedure. I apologize for the extra work and hope for your continuous brisk participation.

All the best.
Ben


Re: BONSAI Updates #meetingminutes #communication

Matteo Lissandrini (AAU)
 

Currently the endpoint is running on a VM at AAU.
(which is quite hard to reach since you need two different steps VPN+proxy machine access)

I think Benjamin is talking about machine independent from AAU.

Also, it is important to note that the requirements (which are not so large by todays standards -- Thanks Moore!) are just if you plan to convert the entire Exiobase.

If you plan to work on YSTAFDB you can do it with your laptop.



---
Matteo Lissandrini

Department of Computer Science
Aalborg University

http://people.cs.aau.dk/~matteo






________________________________________
From: main@bonsai.groups.io <main@bonsai.groups.io> on behalf of Søren via groups.io <loekke=plan.aau.dk@groups.io>
Sent: 23 October 2020 14:52:18
To: main@bonsai.groups.io
Subject: Re: [bonsai] BONSAI Updates #communication #meetingminutes

In principle we should have a VM at AAU (funded by the ODA-project), but I do not know if it accessible and set up in a way that makes this possible(?) Maybe Matteo knows?


Re: BONSAI Updates #meetingminutes #communication

Søren
 

In principle we should have a VM at AAU (funded by the ODA-project), but I do not know if it accessible and set up in a way that makes this possible(?) Maybe Matteo knows?


Re: BONSAI Updates #meetingminutes #communication

 

Holy moly! The hardware requirements are intense. Do we have something like a central BONSAI cluster where we can run such code?

Requirements

To run all scripts, a machine running Linux needs to be installed. The machine should atleast have the following specs:

  • Software;

    • Linux Ubuntu 18.04 Distribution (with git, bash, unzip, wget and docker)
    • Python 3.6+, pip and virtualenv
  • Hardware:

    • RAM: 64GB RAM
    • DISK SPACE: ´~500GB Free
    • CPU: 8 cores


Re: BONSAI Updates #meetingminutes #communication

 

Hi everyone,

I am looking for someone to manage the doodle polls for the next two weeks while I am on holiday. So far, it looks like no action will be necessary as most participants have voted for dates in mid-November. This could change any time though as the ARIES members have not yet given their vote. Anyone willing to organize a meeting in case early November turns out favorable?

Cheers.
Ben


Re: Where can I find (or make) turtle files? #dataliberation

Matteo Lissandrini (AAU)
 

Hi Arthur, all,

the BONSAI conversion workflow is currently ongoing an independent reproducibility assessment in coordination with the ISWC Conference.

Hence, we have setup a way for anyone to get all the data and do all the conversions (Exiobase and YSTAFDB).

Here are the full instructions:

https://github.com/IKnowLogic/BONSAI-reproducibility

If you find any problem, feel free to open an issue on the repo there.

Note that files `.ttl` `.nt` and `.rdf` are equivalent and one can always move from one to the other in any direction automatically.


Best,
Matteo

---
Matteo Lissandrini

Department of Computer Science
Aalborg University

http://people.cs.aau.dk/~matteo






________________________________________
From: main@bonsai.groups.io <main@bonsai.groups.io> on behalf of Agneta via groups.io <agneta.20=gmail.com@groups.io>
Sent: 21 October 2020 21:41:48
To: main@bonsai.groups.io
Subject: Re: [bonsai] Where can I find (or make) turtle files? #dataliberation

Hi Arthur

Here's are the instructions to help you convert Exiobase Supply and Use tables into RDF format

https://github.com/BONSAMURAIS/EXIOBASE-conversion-software <https://github.com/BONSAMURAIS/EXIOBASE-conversion-software>

Cheers

Agneta


Re: Where can I find (or make) turtle files? #dataliberation

Agneta
 

Hi Arthur

Here's are the instructions to help you convert Exiobase Supply and Use tables into RDF format 

https://github.com/BONSAMURAIS/EXIOBASE-conversion-software 

Cheers

Agneta


Re: Where can I find (or make) turtle files? #dataliberation

 

Hi Artur!

Disclaimer: I am not an ontology expert either. I did not see an LCI in ttl yet but you can find some examples of ttl-formated data from BONSAI here: https://github.com/BONSAMURAIS/rdf. For example, you can see how Exiobase has been converted and split according to the key ontology concepts like activity, flow, location, etc. One thing I could not find are the actual numerical values of the flows. Are they stored separately?

Cheers.
Ben


Where can I find (or make) turtle files? #dataliberation

arturdonaldson@...
 

Hi all,

I am looking for semantic formatted data in the form of turtle (.ttl ) files. I tried the SPARQL enpoint but only saw a way to download the results in .csv format.

I am not very familiar with file types used on the Semantic web, so forgive me if this is a silly question, but could someone share a link to some Life Cycle Inventory data in .ttl files?

All the best,
Artur Donaldson

--
LCA Data Scientist
Pre Sustainability
Netherlands


Re: BONSAI Updates #meetingminutes #communication

 

Dear all again,

  1. Nice! Cannot wait to see the presentations! Will they be recorded?
  2. Welcome Rudra! :)
  3. Thanks for the wrap-up, Agneta! As announced, here are two doodles:
    1. to find a date to discuss opportunities for collaboration between ARIES and BONSAI: https://doodle.com/poll/8bpc4uebp3q4gs89
    2. to find a date for the k.LAB tour: https://doodle.com/poll/fdi6c43ad7gyt44k

As before, all options cover the 17:00-18:30 CET time slot, which works for Ken (located in Colorado). Please let me know if none of the dates/times work for you (Massimo?). I will then contact Ken and add further options if possible.

Happy voting!
Ben


Agneta
 

Dear All

Hope you are all keeping in well. We have some updates on recent BONSAI activities :

1) We are presenting our ontology and its application across several virtual conferences:
  • 'Transparent Sharing and Integration of Life Cycle Sustainability Data with Provenance' - Oral presentation by Emil R Hansen at the International Semantic Web Conference 2020. (2nd November 2020)
  • 'FAIRification of LCA data using Semantic Web' - Oral presentation by Agneta Ghose at Brightcon 2020- Open Sustainability Conference (20th October, 2020)
  • 'Modelling LCA data on the Semantic Web' - Oral presentation by Agneta Ghose at LCA Food 2020  (14th October 2020)
2) We welcome a new member Rudra Pratap Deb Nath. Rudra has recently completed his PhD at the Department of  Computer Science, Aalborg University. His research was on the development of integrated platform for semantic business intelligence. He will be continuing his Post Doctoral research at the Danish Centre for Environmental Assessment, Aalborg University. He is extremely enthusiastic to continue the work done for BONSAI from AAU.

3) Last friday (16th September 2020), we had an introductory meeting with Ken Bagstad (Research Economist, USGS’ Geosciences & Environmental Change Science Center ). He is involved with the development of data and models for the  Artificial Intelligence for Ecosystem Services(ARIES) project, which has developed web-accessible and stand-alone software tools to assess ecosystem services for environmental decision-making. The AIRES project members have been working with the use of semantics and machine reasoning to enhance data discoverability for several years. They are keen on further discussions on collaborations with BONSAI. We can potentially have another meeting this November to discuss the possibilities for collaboration. 

Moreover, they are happy to provide an exclusive workshop for BONSAI members on the use of their k.LAB software - A specialized tool to import, annotate, and publish data and models on the k.LAB semantic web, which makes them easier to share, reuse, and link. Our member Benjamin Portner will be in correspondence with all of you to find a suitable date for the workshop. 

Best wishes
Agneta Ghose


Re: Exchange with the Integrated Modelling Partnership #poll #communication

Agneta
 

Dear Benjamin

Thank you for organizing this. I can volunteer to give a short overview of the work we have been doing. 

Best wishes
Agneta


Re: Exchange with the Integrated Modelling Partnership #poll #communication

 

Dear BONSAI-Samurais,

Here is a short update on our exchange with the Integrated Modelling Partnership (IMP):

  • Looking at the doodle poll, most people are available tomorrow, Friday, 16 October 2020, 17:00-18:30 CEST. I therefore ask you to block this timeframe in you calendar. I will also sent out invitations via my organization's Webex shortly. From IMP side, only Ken Bagstad has time to join but I believe this is fine for a first introduction.
  • Concerning tomorrow's agenda, I have none. I suggest we keep it informal, starting with a short personal introduction round, followed by an introduction of our organizations. For the latter part, I am looking for a volunteer who can present BONSAI. I am relatively new and I do not have a complete overview, let alone slides to present. Anybody more senior feeling up to the task?
  • @Massimo and anyone who cannot make it: Let me know if you have any specific question so I can ask them for you tomorrow.

Let me know if you have any open questions or comments.

Cheers.
Ben


Exchange with the Integrated Modelling Partnership #poll #communication

 

Dear BONSAI-Samurais,

Bo brought to my attention the Integrated Modelling Partnership and their technology for the assessment of ecosystem services, ARIES. I believe both, the partnership and the technology, are of great interest to our cause, which is why I contacted the partnership to arrange an online get-together. Ken Bagstad of ARIES answered that they would be happy to meet us. I invite you all to participate in this doodle poll to find a date for a mutual introduction. Because Ken is located in Colorado, potential meeting hours are in the late afternoon. I hope that this will not hamper participation on our side. I will close the poll by Friday, 12. October, 00:00. Please participate numerously! :)

Cheers.
Ben


DataCommons, a.k.a.., we are not alone with this vision #communication

Matteo Lissandrini (AAU)
 

So, sometimes people ask  what is this vision about (and how Semantic Web fits in the picture)?

Some people in the DataCommons initiative provided some more details on that (in a more general domain):

> Publicly available data from open sources are a vital resource for students and researchers in a variety of disciplines.
> Unfortunately, processing these datasets to make them useful --- scraping, cleaning, normalizing, joining --- is tedious, error prone and has to repeated by every group.
> DataCommons attempts to alleviate some of this pain by synthesizing a single Knowledge Graph from many different data sources.
> It links references to the same entities (such as cities, counties, organizations, etc.) across different datasets to nodes on the graph, so that users can access data about a particular entity aggregated from different sources.
> Like the Web, the DataCommons graph is open - any user can contribute data or build applications powered by the graph.
> We are jump-starting the graph with data from publicly available sources such as CDC, Census, BLS, FBI, etc. and are looking to engage with the academic community to take it further.

Here the slides
https://web.stanford.edu/class/cs520/abstracts/guha.pdf


Re: Milestone: Data and workflow reached first stable and tested version #dataliberation #exiobase #ontology #rdf #toolbox

Miguel Fernández Astudillo
 

Congrats :)

I am really looking forward to linking it to some characterisation factors and give a try to produce some impact assessment scores.

Have a nice weekend!

Miguel



On Fri, 10 Jul 2020 at 15:47, Matteo Lissandrini (AAU) <matteo@...> wrote:
Hi all,

"annuntio vobis gaudium magnum", a.k.a., great news!

The BONSAI RDF codebase reached a quite stable and tested stage (more details are provided at the end of the email, don't miss them!) and we have published all the data in the endpoint alongside an updated ontology and a nice interface to query the data.

This result is thanks to great teamwork by many within BONSAI, but I would say is mainly thanks to the tireless and competent supervision by Agneta and the copious sweat of the fingertips of Emil.
Please join me in thanking them for this notable effort.

Now comes the great opportunity by BONSAI to capitalize on this: test the queries, write new queries, try to improve the tools, introduce a new dataset, but first of all maybe start with adding more examples and tutorials for newcomers.

So, why am I so happy? What do we have now?

- The data is *fully* reachable at odas.aau.dk
     * the endpoint contains all the data (more on that below)
     * we moved from Jena to Virtuoso, still opensource, but much more performant
     * there is a nice GUI that allows to run a number of example queries (also called competence queries)

- Thanks to the competence queries and the GUI Agneta found out that the USE/SUPPLY tables in Exiobase were not square (Agneta can explain this in the correct details) what is important for me to highlight is that our improved accessibility to the data allowed to rectify a fundamentally wrong assumption we had about the Excel files. Huzza for Open Data and Accessibility to the data

- About the data, we now have exported and host _2_ datasets: Exiobase (+emissions) and YSTAFDB, both matching to the same ontology

- The ontology has now moved to v2 since we support now balanceable properties (and also we adopted a more intuitive terminology)

- We introduced in the extraction code (and consequently in the published data) annotation for provenance. Now data providers integrating new datasets can ensure traceability of each piece of information.

-  This has resulted in various improvement and extentions of the Arborist code.

- Also, with the inclusion of the YSTAFDB we have tested the workflow required to incorporate new datasets.

- Tomas is working on the final piece of the puzzle to transform this Open Data in truly Linked Open Data.


As a result of this process we submitted an experiences paper to the international conference of semantic web to share the challenges and the lessons learned during this effort (fingers crossed the reviews are out soon!)

My understanding is that Agneta is also leading a paper writing for a LCI journal about this resource, I will let her update us on the status of that other paper. Nonetheless, I think we should definitely publicize this resource as much as possible.


With this milestone reached, Emil will have to move to a different project, so at least in the short term he will not be able to spend any more time on this (actually he already delayed other pressing matters in order to complete all the tasks here and some extra that we did not foresee, thanks Emil!), but I will be always available for questions and I know where he sits in case, so please contact me instead for SW related issues ;-)


Hence, once more: please play with the GUI, run some queries, write your queries, read the documentation.
Check open issues or open new ones and then try to fix them.
Especially if you see ways to improve the documentation, give it a try yourself and ask me or Agneta to review your work, this is the best way to get to know what we have! This has to be a community effort now.
This is the opportunity for anyone interested to start playing with this rich resource and keep improving it.


Again, great work, let's keep progressing and opening more data to the world.


Best wishes,
Matteo





---
Matteo Lissandrini

Department of Computer Science
Aalborg University

http://people.cs.aau.dk/~matteo