On the different types of interoperability and the concept of agricultural data

I have been involved in various instances where interoperability between different sources of content was the main issue - ranging from the early days of enriching the Organic.Edunet Web portal and collections with content from external sources (such as the OER Commons Green collection) to complex content aggregation workflows of heterogeneous data in the context of the agINFRA FP7 project (the project that gave birth to AGINFRA) and a recent contract with UN FAO regarding the status and potential of various levels of interoperability in the fisheries and aquaculture sector. All these instances allowed me to get to know more about metadata schemas and vocabularies, standards for exchanging metadata, digital repositories and how they communicate with each other, mapping and transformation of metadata schemes to another standard etc.

I was recently invited to complete a questionnaire regarding open data standards and that brought me back to the basics; what are the different types of interoperability that exist out there? I could very quickly think of the following:

• Semantic interoperability, referring to the use of standards for the description (metadata) and the classification (Knowledge Organization Systems such as vocabularies) of data;
• Technical interoperability, referring to the use of standards for the exchange of data, such as the OAI-PMH standard for metadata but also the use of standard file formats for sharing data (e.g. XML, CSV, JSON etc.);
• Legal interoperability, referring to the use of standard licensing schemes, which would facilitate the exchange of data in legal terms.

There may be a couple more out there but time is short for such an academic analysis.

 (Image source: https://xkcd.com/927/)

The same questionnaire referred to “standards for food and agriculture data”; but what exactly are agricultural data? One (including me) could argue that there may not be "food and agriculture data" as different data types. I have been through similar discussions in the past; however, it seems that there is no such thing as "food and agriculture data". This only refers to various types of data that are used in the agrifood sector or are produced in the agricultural context. In this context, “standards for food and agriculture data” are the same as the rest of the data, such as the standards applying to economic, statistical, trade, weather forecasts, soil maps, sensor data, weather forecasts, earth observation data, demographic, bibliographic, metadata etc. It is usually only the context that changes - not the standards or the data themselves.

If we accept this generic point of view, then standards like ISO (see for example the ISO/IEC 11179 standard), metadata standards like Dublin Core, file format standards like ODF, classification standards like OWL and linked data standards like RDF could also be applied in the case of agricultural data. The same goes for technical interoperability standards like OAI-PMH and REST APIs; all these can be (and actually are widely) used in the agricultural sector and are essential tools for those of us working with agricultural information and knowledge management.

So, are there really agricultural data and if so, who could name some examples?

Call for Papers: 10th International Conference on Metadata and Semantics Research (MTSR’16)

The 10th International Conference on Metadata and Semantics Research (MTSR'16) will be held at the Food and Agriculture Organization of the United Nations (FAO) in Rome (Italy) on November 22-25, 2016. Traditionally, MTSR brings together scholars and practitioners with common interest in the interdisciplinary fields of metadata, data and semantics. The conference provides an opportunity for participants to share knowledge and novel approaches in the implementation of semantic technologies across diverse types of information environments and applications, such as Cultural Informatics, Open Access Repositories and Digital Libraries, E-learning applications, Search Engine Optimization and Information Retrieval, Research Information Systems and Infrastructures, e-Science and e-Social Science applications, Agriculture, Food and Environment, Bio-Health & Medical Information Systems.

This year, MTSR’16 celebrates the conference’s 10th anniversary with the theme of bridging the past, present and future of metadata, data and semantic technologies. The organisers encourage prospective authors and conference participants to reflect on the following questions:

• How the documented evidence produced over the past years can be used as a driver for innovating management and processing of data and information?
• How close are we from the vision of building powerful learning systems that will meet the needs of modern societies through high quality data infrastructures and data-driven interfaces?
• What are the main challenges that modern metadata and semantics research has not addressed yet?

What is of interest to our agrifood community is the Special track on Metadata and Semantics for Agriculture, Food & Environment (AgroSEM'16), which aims to bring together researchers and practitioners that are dealing with theoretical, methodological, experimental and application-oriented aspects of knowledge engineering, applied to agriculture, food and environment. This year, AgroSEM is chaired by Juliette Dibie & Liliana Ibanescu from AgroParisTech & INRA and we kindly invite anyone to contribute with a submission on metadata, semantics and related topics always in the field of agriculture, food and the environment. Agroknow has a tradition in participating to AgroSEM either through submissions or through contributions to the Programme Committee.

If you are interested in submitting a paper to MTSR 2016/AgroSEM 2016, you need to check out the following deadlines:

15th May 2016 : Submission deadline
30th June 2016 : Notification of acceptance
10th July 2016 : Camera-ready papers due
22nd – 25th November 2016 : Conference at FAO of the UN (Rome, Italy)

You can find detailed information about MTSR 2016, such as practicalities and submission processes, on the event's website.

PubAg: Providing Open Access to agricultural research

PubAg is the National Agricultural Library's (NAL) search system for agricultural information. It provides access to quality agricultural research publications both from USDA-affiliated researchers as well as from external ones. authored and other highly relevant agricultural research. When it was launched, it started with a number of 40,000 full-text journal articles provided by USDA staff  and including about 450,000 citations to both internal and external publications. The aim of the National Agricultural Library is the enrichment of the available content on a monthly basis, by adding about 20,000 citations each month.

PubAg provides access to full-text articles relevant to the agricultural sciences, along with citations to peer-reviewed journal articles. Each resource is described with metadata, including

• Title
• Abstract
• NAL terms: They are clickable, so by clicking one of them, you get a list of results tagged with the specific term.
• Names of Authors: They are clickable, so by clicking one of them, you get a list of results from the specific author.
• Citation
• Link to the publisher's record (through DOI): The link can be used to access the metadata record of the publisher and hopefully the full-text article, if it is openly shared (i.e. it is not available behind a paywall).

In addition, each metadata record can be exported as CSV or printed; in the latter case, the user receives a printer-friendly version of the metadata record.

A metadata record in PubAg

On the other hand, when a user want to perform a query with specific terms, he can use a free-text search box. Words entered into the search box are automatically translated into subject terms from the NAL Thesaurus (NALT) and the corresponding documents tagged with these NALT terms are retrieved and presented to the user.

List of results after a query

As of today, PubAg provides access to about 972,000 metadata records and 42,000 full-text articles. 200,000 records reflect on research published after 2012, which makes the content really up to date.

 I was also surprised to find a few of my publications on the PubAg portal!

Who would have thought...(some of) my publications available through PubAg!

Thanks to the ongoing work related to GACS (Global Agricultural Concept Scheme), this large database of quality agricultural research outcomes will be easily interconnected with others, such as the FAO AGRIS (that Agro-Know is maintaining and expanding, boasting almost 8M records) and the CAB Abstracts (about 2M records). This is expected to greatly facilitate the work of agrifood researchers, information and knowledge managers, among others.

Turning three thesauri into a Global Agricultural Concept Scheme from CIARD Movement

RDA 3rd Plenary Meeting - Day 1

The 3rd Plenary Meeting of the Research Data Alliance (RDA) took place between 26-28/3/2014 in Dublin Ireland. It would be my 2nd participation in a row to an RDA plenary meeting and I managed to organize my trip (even at the last moment) and be there. It was not an easy trip, as I had to travel to Dublin from Athens on a Greek national holiday/celebration but still I did that. The trip itself was nice, reaching Dublin through Copenhagen (with SAS) and then reaching Athens through Frankfurt with Lufthansa; it was my first time in Dublin but due to the packed schedule of the meeting and the moody weather I did not get to see anything outside my 20 min walk from the hotel to the meeting place (at lovely Croke Park) and back.

Statistics about the 3rd RDA plenary
477 participants registered and attended the meeting. The overall RDA membership is 1,585 from 71 countries (64% from academia; 49% EU, 37%US; 2% policy makers).

About the venue
The meeting was hosted at the Croke Park, which is a nice combination of a football stadium and an exhibition center - a fully equipped one I have to admit; the plenary sessions took place at a large hall which fitted the almost 500 RDA meeting participants nicely while coffee and lunch breaks took place right outside the hall. I wouldn't want to know more about the logistics (taking care of such a big number of participants for catering etc. must be a hard task) but the organizers did a great work. There were some issues with the wifi connection but the technicians were working on them as well as lack of power outlets in the big hall (which left a high percentage of the laptops used by the participants for tweeting etc. off after the first couple of hours!) but in the end everything was fine.

Agro-Know was there, with folders including interesting brochures and company profile 1-pagers. In addition, the agINFRA project was disseminated through discussions and the brochures; I also managed to arrange having the 3 small agINFRA project posters to be placed in the poster session just a couple of hours before the poster session, When there's a will there's a way, as they say ;-)

Day 1 Plenary Session
The plenary session started with keynote speeches and greetings; I personally enjoyed more the Keynote Address by Prof. Ian Chubb AC, Australia's Chief Scientist. Some of his key-points, as extracted by various tweets were the following:

• We need national, international and inter-disciplinary collaboration in research and innovation;
• We need research and data to be able to feed 9 billion people, producing carbohydrates and fiber while climate moves;

You can also watch his presentation recording here.

Additional presentations/speeches took place afterwards, mostly highlighting the fact that data exist and it is up to the users to find a meaningful way to use them and that infrastructure is already here, waiting for useful applications. The highlight was a cartoon presented by Dr Ross Wilkinson, Executive Director, Australian National Data Service, showing a donkey, a cart and a carrot; an image really familiar to many of us. This led to nice and funny discussions as well as an explosion of related tweets!

Day 1 WG/IG sessions

I opted to attend the "BoF Education and skills development on Data Intensive Science" organized by Yuri Demchenko and Wouter Los, which aimed to identify opportunities for the new field of data scientists. My colleague Miguel-Angel Sicilia from the University of Alcala was also there, proposing his approach on the subject and discussing the possibility of an interest group, a proposal of which has already been submitted. Discussions were interesting and focused on the existing curricula all over the world.

Next was the meeting of the Agricultural Data Interoperability IG, which was chaired by agINFRA colleagues Johannes Keizer (FAO) and Devika Madalli (Indian Statistical Institute, Bangalore). There I made a presentation titled "Global RDF Descriptors for Germplasm Data", describing the work done in the context of the agINFRA project and the RDA WG towards the exposure and publication of germplasm data as linked data (always based on the work already done by other experts in this field).

It was followed by another presentation by Esther Dzale from INRA, about the Wheat Data Interoperability Working Group and then there was a discussion on various topics affecting the group.

Reception sponsored by Irish Research Council gave us some time to get to meet new people and have interesting discussions; I managed to meet

• Nikos Houssos from the Hellenic National Documentation Center who are working with the aggregation of metadata from various Greek repositories, among others;
• Nuno Freire, Chief Data Officer at The European Library, with whom we discussed about the role of a CRM tool in the metadata aggregation workflow
• Stephane Goldstein from the Research Information Network (UK), with whom we had an interesting discussion about the proposed IG on Education for Data Scientists
• Odile Hologne, Head of Scientific Information Dept. of INRA, who has been in long communication and collaboration with AK but we never had the opportunity to meet in the past;
• Phil Archer from W3C (the previous time was in the 2nd RDA Plenary in Washington D.C. last September), who was disappointed by people not following the existing standards for linking their data! 

Hearing people talk about using non-URI identifiers to link people to papers and datasets ... is painful #RDAPlenary

— Phil Archer (@philarcher1) March 26, 2014

In addition I got to see again old time friends like Johannes Keizer from FAO, David King from Open University (last time we met was back in May 2012 in the 2nd BioVeL workshop in Gothenburg, Sweden!), Esther Dzale from INRA and others. It's always nice to be among friends in such big events!

More info about the 3rd RDA Plenary:

• List of participants
• Programme
• Dissemination material
• You can follow the updates in Twitter using the #RDAPlenary hashtag

1st International e-Conference on Germplasm Data Interoperability: Session 2

Session 2 of the 1st International e-Conference on Germplasm Data Interoperability themed "Status of data and metadata for germplasm" included presentations on the metadata standards used in the various germplasm data sources, presentations of germplasm data providers and aggregators of germplasm data as well as people who have been working with germplasm metadata. It was deployed using Google Hangouts, thanks again to +Luca Matteis who made all the necessary preparations and organized the Hangout. Despite the fact that it was the second time that we used this platform, we still had some issues like desktop sharing not working, participants disconnecting etc.

The session started with a very quick introduction to the Conference (again) by me; this time I was better prepared and had some more time to introduce participants to the scope of the Conference and the presentations of this 2nd session. The first presentation was made by +Matija Obreza from Global Crop Diversity Trust, who made a presentation of the GENESYS Germplasm Data aggregator. The next presentation (more in the form of discussion) came from +Theo van Hintum and +Milko Škofič who presented the case of the EURISCO germplasm data aggregator and the experience related to metadata adn data sharing between European genebanks. The next presentation was to be delivered by +Maria Antonietta Palombi, (from CRA) about the Italian National Germplasm Database; however, this was not possible due to constant connection issues. +Dag Endresen made a presentation of the Global Biodiversity Information Facility (GBIF) followed by my presentation about the germplasm metadata analysis that we did in the context of the agINFRA project.

agINFRA Germplasm metadata analysis from Vassilis Protonotarios

What I found really interesting about this session (apart from the presentations themselves) was the elaborated discussion among (mostly) the presenters; this was expected, as interesting issues were raised during the presentations. In addition, thanks to the use of the Google Event page, there were a number of comments and links shared between the participants, which was also useful and drove the discussion.

The recording of the 2nd Session is available through YouTube as it was automatically recorded; another convenience provided by Hangouts, while the presentations are available through the event's website.

I believe that this 2nd session was more well-implemented than the 1st one, despite the issues that we faced. Session 3, which will take place on 19/12/2013, will be asynchronous, meaning that presentations will be recorded as videos and shared with the participants of the Conference - there will be no live streaming or coordination. We hope that there will be some comments related to each presentation. Until then, stay tuned!

agINFRA users' meeting, 26-27/3/2013

AK hosted the agINFRA users' meeting in Athens, between 26 and 27 of March, 2013. The meeting was attended by the majority of the agINFRA data providers and gave the opportunity for discussion about the next steps in the context of WP5, which is related to data aggregation. I was really involved in this meeting, as it was an excellent opportunity for me to collect feedback on the D5.2 "agINFRA data integration methodology and workflow" and D5.3 "Conceptual specification of linked agricultural data integration layer", which were ongoing during this period but still there was input missing.

Hands-on session during the meeting

As regards D5.2, we had a great time with the data providers trying to depict their own (meta)data management workflows using flipchart sheets and markers and at the same time trying to see which of the collections we could use at this first metadata ingestion step. In D5.3 things were less fun, as we had to discuss about any type of Knowledge Organization System (KOS) such as controlled vocabularies, ontologies and thesauri which is used by the data providers for the classification of the resources but has not been published yet. This will be a challenging task, requiring a cloud-based installation of a KOS management tool and guidance of the partners in uploading their KOSs and linking to existing KOSs, which are already published, in order to facilitate the mapping between the different KOSs.

On top of that, we got to discuss about the tools which may be used for the uploading and puiblication of KOS as well as about the agINFRA integrated services from the users' point of view. As a user I found all discussions to be really useful :-)

The meeting was also an excellent opportunity for me to see again old friends like +Imma Subirats but mostly to meet new people like Davika, +Giovanni L'Abate, Ivana, David and +Valeria Pesce, with whom I have exchanged a lot of emails during the last months but never got to meet them in real life. Even though I was pretty ill during the two days of the meeting (high-fever, probably a flu), I got the chance to get to meet everyone slightly better. On the other hand I missed the opportunity to get to meet Guntram and Jane who did not finally make it to the meeting, people with whom we have exchanged a lot of emails but never had the chance to meet.

A big thank you goes to all those who got involved in the organization of the meeting (I know how hard it is) as well as to those who managed to travel to Athens and provided their feedback during the tow days of the meeting!

Brand-new publication on Metadata - MTSR 2012

It is now official: the paper that I co-wrote with Prof. Roman and and Dr. Maria Toader from the University of Agronomic Science and Veterinary Medicine - Bucureşti, titled: "The Use of Metadata in the Description of e-Learning Content for Organic Agriculture", was accepted in the Fifth International Workshop "Metadata and Semantics for Agriculture, Food and Environment" of the 6th Metadata and Semantics Research Conference (MTSR 2012) and now published in the Springer Proceedings of the MTSR 2012 Conference.

The paper is about a part of the outcomes of the Organic.Balkanet project, and more specifically the training curriculum of the project, and how educational metadata were used for the description of the courses included in this curriculum. The metadata part described in the paper was a long, time consuming and error-prone process, so the results were rather poor; however, we managed to have a first version that was later elaborated and improved by other stakeholders. The paper was also a dissemination activity of the Organic.Lingua project, as the translation and multilinguality issues mentioned in the paper are in the heart of the project. In addition, everything related to Organic.Edunet is now a part of the Organic.Lingua project (including the new collections added to the Organic.Edunet network).

My colleague Nikos Manolis who traveled to Cadiz, Spain and participated in the Conference made the presentation on behalf of the authors. Unfortunately, I could not participate in the Conference due to other obligations at that time but still I was glad to know that my submission was presented. I am really looking forward to receiving feedback on how it went and if there were any questions about that. The paper is also a part of the VOA3R Controlled Experiment for Reviewing Lifecycle Services, so anyone is invited to visit the blog hosting the experiment and review my paper (among others), so that a related (and fruitful) discussion can be initiated.

VOA3R 5th project meeting

I recently came back from Paris, where the 5th project meeting of VOA3R was held during 29-31/5/2012. The meeting was interesting as always, discussing a wide variety of issues including the project's management, quality assurance & risk management aspects, dissemination and affiliation plans and activities etc. My part had to do with the content population activities of the project, as I am a member of the GRNET team which is leading the specific work package. The task is rather complex, since it heavily relies on other WPs, such as the one developing the VOA3R metadata AP, the harvesting and portal parts, the quality assurance and dissemination/affiliation plans.We already had some delays with these tasks but during the meeting we tried to describe the current status and define the next steps for the next months.

Presenting the next content population tasks (photo by Imma Subirats)

It was a nice opportunity for me to meet Diane (since we had to solve some issues for the Organic.Lingua project) and David Martin from UAH who has only recently joined the team and has also helped in the Organic.Lingua tasks.

Panoramic photo of the meeting (photo by Imma Subirats)

Apart from that, I had the opportunity to see Paris and its sights for the first time. I managed to get some hours off and really quickly visit the major sights including the Eiffel tower, the Notre Dame, Champs-Élysées, Monmartre, while I also passed just outside the Louvre, taking photos all the time on the road. Despite the bad weather (it was drizzling all the time) I really enjoyed the evening.
Next VOA3R project meeting is to be held in Cyprus, courtesy of George from ARI!

VOA3R 4th project meeting

Having breakfast at Movenpick Hotel

The meeting is hosted in Izmir, Turkey collocating with the MTSR 2011 Conference in the premises of the Yasar University. The room provided for the meeting looks like a cinema hall, being really comfortable and suitable for presentations at the same time. However, the lack of power outlets created a significant problem regarding the charging of laptops. This was an issue, since the use of laptops was really necessary in some sessions.


It seems that there were a lot of open issues to discuss, including the progress of the tasks and the next steps of the WP5 - Content Population, to which more than half a day was dedicated. The WP5 session was really interesting as it contained presentations on the content part as well as on the more technical part (e.g. the presentation of the VOA3R metadata AP), along with a special presentation by Nikos Palavitsinis from GRNET, who shared his experience on the Metadata Quality Evaluation during the Organic.Edunet project.

VOA3R Family Photo. Izmir, 12/10/2011

In addition, on Wednesday evening the VOA3R Controlled experiment on reviewing lifecycle services will be realized, as the papers submitted to both the 4th International Workshop on Metadata and Semantics for Agriculture, Food and Environment and the VOA3R Controlled experiment will be presented by the authors. I have already dedicated a lot of time and effort to this experiment so I really hope that everything will be ok in the end and the feedback received will be more than adequate.


UPDATE: The controlled experiment went pretty well, despite the difficulties. Almost all papers were presented (I had to make my presentation on the next day) but the hardest part will be to get some valuable feedback about the process followed in this experiment, from both the authors and the participants. In addition, since some of the presentations took longer than expected, so I had to reallocate my presentation to the session of the next morning, just before flying back to Athens! 

CerOrganic ToT School - Day 1

The first day of the school is finally over. It was an exhausting day, as we rushed directly from Chania airport to the MAICh premises in order to attend the first sessions of the school. The lecture hall was crowded with more than 40 participants, being OA trainers, farmers and tutors of the school, among which many CerOrganic project partners.

The first sessions were presented by Dr. D. Smith and Ms. M. Moises (BM:UKK, Austria)

1. Designing a course with e-learning components
2. The importance of planning the e-learning course
3. Discussing the effectiveness of an e-learning course
4. Facilitate and evaluate the course

They were really interactive sessions, providing basic information on various aspects of an e-learning course.

After lunch, it was time for the Agro-Know team. Mr. Charalampos Thanopoulos provided detailed information on more practical issues of the training course, during the sessions:

1. Designing the training course
2. Implementation of participative techniques

Then I had the chance to further elaborate on blended learning methods in the training context, by presenting the sessions:

1. Introduction to the Organic Farmer Scenario concept
2. Elaboration of Organic Farmer Scenario description

during which the participants were introduced to the concept of training scenarios, they were presented with the predefined templates and they were asked to start describing their own training scenario. It seems that the training scenario concept was accepted by the majority of the participants, who started working on this description for the 30 mins that they had available. The flow of information in this sequence of sessions was smooth and continuous, so the sessions were building a solid basis for supporting the concept of training scenarios.

The first day of the school ended with a presentation about metadata and their application in the description of learning/training resources. A hands-on exercise that was intended to take place during this session was moved in tomorrow's program, during the MOLE platform hands-on exercise.

As for some technical issues, even though we faced a slight problem with the availability of power plugs for all these laptops and netbooks used during the course, we faced no problems with the internet connection. It was really weird to see that, as I was used in facing severe problems (or no connectivity at all) during such events....

Tomorrows program includes some more presentations by me, on "Using Open Educational Resources to support scenarios", "Finding digital resources: The Organic.Edunet Web portal", "Elaboration and adaptation of Organic Farmer scenario activities & resources" and "Preparation of Organic Farmer scenario presentation". This will be a 4-hours presentation marathon by me!

More info to come tomorrow.

Meeting Erik Duval

Yesterday I was really lucky to meet Erik Duval for the first time. He was kind enough not only to visit our offices but to make a short presentation about his work and interests. I was really amazed by the things that he's working on as well as by his simplicity and knowledge...he looks like a metadata guru to me! Despite these, he was so kind and friendly.
It was so interesting discussing with him topics that for me were so "daily" and he gave such a different perspective that I wanted to go through my relevant stuff once more and revise them!

It is a good thing that colleagues of mine are collaborating with Eric, so I hope I'll have the chance to meet him again and probably attend one of his presentations face to face.

It was nice meeting you Erik!