Nomenclature Focus Group

 

Navigation News for week 014: 23/11/2022 to 30/11/2022
About:
– Who we are
– Motivation
– Objectives
– Timeline
– Code of conduct
Thematic areas
Resources
Member list
Previous news:
– Week 013
– Week 012
– Week 011
– Week 010
– Week 009
– Week 008
– Week 007
– Week 006
– Week 005
– Week 004
– Week 003
– Week 002
– Week 001
– Week 000
Thanks for all that send some recommendation of researchers in optics/chemistry interaction to be invited to the group. If you have more recommendations you can send to me and Daniela either privately or in the group.

Updates:

  • We had defined the end of November to be our deadline to complete the first version of the deliverable_specification document. However, considering the importance of this document, the need to further discuss some aspects of it, and the likelihood that we will only start the content creation phase in January, we are extending the deadline to conclude the first version of the specification to the end of this year.
  • We have created a type a gantt chart for our milestones to help all navigate or understand the evolution of the project. This document will be updated to give more resolution (whenever we break down a milestone in “sub”milestones).

About


Who we are

The GEO AquaWatch Nomenclature Focus Group is a community-lead initiative to harmonize and make accessible the terminology in hydrologic optics and aquatic remote sensing. It is hosted by GEO AquaWatch and has support of IOCCG. As a focus group, it has limited duration and is expected to be active from August 2022 to August 2024. As of November 2022 it has more than 50 members from a diverse set of specializations, institutions  and nationalities.

It is a volunteer-based effort organized over a variable number of thematic areas and overseen by a general coordination. The two general coordinators are Alexandre Castagna and Daniela Gurlin. The thematic areas currently active and their respective coordinators are presented in detail in the section thematic areas.

The group is open to community members that wish to collaborate with the effort. It is possible to join the effort at any stage stage of the project development. To join the focus group, send an email to Alexandre Castagna and Daniela Gurlin.

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Motivation

Hydrologic optics and aquatic remote sensing are multidisciplinary research areas, often with research groups working within a limited scope but nonetheless dependent on concepts, methods, and quantities from the broader scope encompassing these research areas. For example, concepts of engineering, atmospheric optics, meteorology, statistics and radiative transfer are necessary for robust aquatic remote sensing application and interpretation. Knowledge about phytoplankton pigmentation groups, ecology, genomics, statistics and optical processes is of relevance when considering absorption-based algorithms and their application to phytoplankton diversity. Connecting and leveraging the developments in the different areas requires an accessible and common language.

Jargon exists to simplify communication, but can also act as a barrier when it does not adequately (or intuitively) capture the concept it is intended to encapsulate. For example, as knowledge evolves, nomenclature may need to be updated to better reflect current understanding. It also seems the case that at least some nomenclature was created without special attention to existing terms in related fields, or care about its specificity (e.g., ‘anomalous diffraction’), or objective definition (e.g., ‘optically shallow’). It is also the case that some definitions or terms vary between research groups / traditions, or are currently evolving in the literature. It is also encountered that some terms referring to theoretical definitions are indiscriminately applied to measured quantities, despite the known departure from definitions (e.g., attenuation and scattering coefficients). Even if none of those were issues, the terms and definitions we interact with are not concisely and systematically collected in a reference document.

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Objectives

The main objective of the GEO AquaWatch Nomenclature Focus Group is to provide a free and accessible authoritative terminology reference that can facilitate communication between researchers with different specializations and experience within the field, researchers from closely related fields and stakeholders (institutions, agencies, etc).

The agreed upon key features of a deliverable addressing this objective are:

  • Authoritative: accurate, rigorous, community consensus, and endorsed by major hydrologic optics and aquatic remote sensing institutions or organizations;
  • Comprehensive: include a broad selection of terms and concepts encompassing the multidisciplinary research field and closely related research areas.
  • Focused on interpretation: provide clear links between theoretical and measured quantities, provide information on range of observed values in natural environments, and other information that improves the interpretation and use of measured and estimated quantities.
  • Online and free: for easy access, low cost of production and distribution, flexible downloadable or printable.
  • Enhancing discovery: interlinked, searchable, machine readable, built in ontology.
  • Citable: provide support for articles and projects, not needing to define terms and symbols, but point or link/embed directly the content.
  • Promote and facilitate use: provide enhanced user interaction such as the export of equations and symbols in vector format, LATEX code, API for synonyms and data conversion, etc.
  • User friendly: provide an intuitive interface for authors, editors and readers, use an accessible color scheme when considering color vision deficiency, potentially include a programming interface, among others.
  • Machine readable: enable semantic web applications.
  • Built with expansions in mind: for example, multi language support.

Based on the above objective and key points, the Nomenclature Focus Group will produce and curate a version-based online encyclopedia, powered by the MediaWiki software and its Semantic MediaWiki extension. Content creation, editing and reviewing, will be restricted to the Nomenclature Focus Group members.

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Timeline

The overview of the agreed upon timeline of the project is provided below.

NFG Timeline. Project duration of two years. The first three months are devoted to organize the members in thematic areas and list entries to be curated and main references, while also defining styles and creating the necessary infrastructure. The following eighteen months will be dedicated to content creation and the last three months will be dedicated to community review of the final product.
GEO AquaWatch Nomenclature Focus Group timeline. November 2022.

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Code of conduct

The Nomenclature Focus Group will follow the same code of conduct adopted by GEO AquaWatch (in preparation). The document will be linked here when available.

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Thematic areas

To better organize the effort, the Nomenclature Focus Group is subdivided in thematic areas proposed by its members. The list of thematic areas and coordinators is provided below:

NFG Organogram
GEO AquaWath Nomenclature Focus Group organogram. November 2022.

To join a thematic area first you need to be a member of the Nomenclature Focus Group. To join the focus group, send an email to Alexandre Castagna and Daniela Gurlin. As a member you can edit the thematic area membership file by adding your name to the desired thematic areas.

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Resources

The main resources used by the group are a mailing list and a shared folder for administration and planning. The content under production is contained in a private wiki that will be published with the release of version 1. Some of the relevant documents are available here:

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Member list

General coordinators:

Thematic area coordinators:

Members:

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Previous news


Week 013: 16/11/2022 to 23/11/2022

Thanks for all that could attend the presentation on the Semantic MediaWiki today. Soon the link of the video will be made available to others in the group that could not join and are interested in knowing more about the platform.

I have prepared a distilled summary below of what MediaWiki and Semantic MediaWiki are (in my understanding) and why I think they are the platform of choice for our deliverable. If you have any questions, general or very specific, or would just like me to elaborate more, please send a message to our mailing list.

We will have a hands-on session where we will show the actually very simple interface to write content to the platform (or copy and paste from your own computer).

Summaries:

  • Today we had a presentation by Bernhard Krabina, about Semantic MediaWiki. I got the impression it was more technical than most of us were prepared for, assuming little background in the MediaWiki ecosystem and semantic web. So I would like to summarize a bit, assuming that most have accessed Wikipedia, the most famous wiki running MediaWiki: MediaWiki is a powerful software for collaborative content creation and includes out of the box many features we desire for our deliverable. Sematic MediaWiki (SMW) is an extension to MediaWiki that provides a method for structuring information, using concepts of the so called semantic web. Semantic web is based on the idea of triples: subject + predicate + object (e.g., Radiance has units of W/m2/nm/sr, where “Radiance” is the subject, “has units of” is the predicate, and “W/m2/nm/sr” is the object). In SMW, the subject is the page containing the information, the page Radiance about radiance, the predicate is the property, “has units of” – which is defined in its own page Has units of, and for page Radiance it has value of “W/m2/nm/sr”. This is what makes it machine readable, structured information which is a form of database. But instead of having this in a spreadsheet of sorts, this is merged with the text. As a database, we can query and extract this information. For example, internally we can import the value of a property “has symbol” from the page Radiance to another page we are writing and mentioning radiance, and so any change in the value of the property “has symbol” for the page Radiance would automatically propagate to all pages importing its symbol. This information can also be used externally, say a webpage importing the value of “has symbol” (say a community data portal like SeaBASS or Limnades) or a document editor that allows for this kind of import (say, when writing a paper or report). Data itself, dates, authors, coordinates, can all be queried and displays (like plots) are made automatically by adding a query code to a given page. Further, search engines such as Google give preference to structured content that are referenced against its own set of vocabularies (Schema.org). And in our own field we have sets of vocabularies of other institutions – this provides a machine readable way to indicate synonyms of properties and their values, data units and conversions, etc. Within our group I took the responsibility of evaluating and learning about the platform we would use for the deliverable. Most of this is new to me, but from what I learned so far, MediaWiki and SMW are a fit for purpose for our application (including listing page authors, exporting to bibtex, version control, persistent identifiers, mathematical rendering, iterative graphics, RDF link in the HTML version of a page, etc). Members of the group do not need to have background or understand any detail or technical aspect of this, only those who are particularly interested or volunteer to help with the infrastructure. This presentation was intended to provide a high level overview of what this platform can offer and how it fits, out of the box, our case.

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Week 012: 09/11/2022 to 16/11/2022

This week we welcome:

  • Ariel Blanco from PhilSA / EnviSAGE (PH)
  • Claudio Barbosa from INPE (BR)
  • Mariana Soppa from AWI (DE)
  • Philipp Saile from GEMS / ICWRGC (DE)
  • Tadzio Holtrop from PlanBlue (DE)
  • Vitor Martins from MSState (US)

Updates:

  • Next week we have the presentation about the Semantic MediaWiki by Bernhard Krabina, November 23, 15:00 to 16:00 UTC.
  • The minutes of the 2nd plenary meeting are online for review. To further help new members to better understand the initiative, the recording of the 2nd plenary meeting will be available for the next few weeks.
  • Don’t forget to review / contribute to the draft of the deliverable specification. It is open for contributions until November 30. Please add those contributions as comments or edit the document with the option “suggesting” (set the drop down menu at the upper right corner).

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Week 011: 02/11/2022 to 09/11/2022

This week we welcome:

  • Daniel Maciel from INPE (BR);
  • Dariusz Stramski from UCSD (US);
  • David Antoine from Curtin (AU);
  • Hà Nguyễn from VNU (VN);
  • Janet Anstee from CSIRO (AU);
  • Nathan Dryason from CSIRO (AU);
  • Salem Ibrahim from KUAS (JP);
  • Shenglei Wang from RADI (CN);

Updates:

  • The draft of the deliverable specification is open for receiving contributions until the end of November for a first version. Please add those contributions as comments or edit the document with the option “suggesting” (set the drop down menu at the upper right corner). The idea is to document how and why the deliverable will function and it contains the base propositions brought up by the coordination in the last meeting. Some of the topics, as a citation model, needed some further discussion. Some more technical aspects of the document, relating to implementation in MediaWiki are in early draft stage and will be evolving fast the next few weeks. Unless you are interested in the mechanics of MediaWiki, you can ignore those parts.
  • The coordination would like to thank all members that send suggestions of researchers that we should reach out to, with special attention to researchers in institutions from countries or geographic regions that are underrepresented in this group. In total, 34 invitations have been sent since the meeting last week.
  • We have decided to test a simple method for thematic area communication. To indicate that a thread is sent to the members of a specific thematic area, members creating the email thread are requested to add the group prefix to the subject line as “GXX: “, where XX is the two digit group number as defined in the thematic_areas_membership file.
  • Samantha Lavender is now coordinator of the Earth observation thematic area. We are looking for another volunteer to share the coordination with her.
  • Tristan has started an entry on polarization discovery, as part of the historical notes thematic area.
  • Daniela Gurlin is making the careful work of writing the minutes of the 2nd plenary meeting. This is the reference document and will be available by the end of this week, but a summary is provided below.

Summaries:

  • We would like to thank all that participated in the 2nd plenary meeting last week. Due to special circumstances or time zone constraints not all members could join and we also appreciate the communication and suggestions we received from those.
  • An evaluation of the progress since the first meeting showed that we are mostly on track, though we are behind in: prototyping (producing one or two example entries per thematic area), on listing entries (concepts, quantities, methods) that will be curated by each thematic area, and on having filled coordination positions in all thematic areas. Currently optics, benthic habitats and Earth observation have only one coordinator each and biology and geology have no coordinators – any volunteers in the group? We have a draft document describing the coordination positions. The example entries are very important for us to have a clearer view of the format/structure of the entries.
  • We have proposed a citation model to address concerns by the members on attribution and recognition for the volunteer work. Essentially each entry could be cited individually, with authorship automatically listed if so desired. This is detailed in the deliverable specification.
  • We have also proposed a production model to separate the technical aspects of managing the information, creating texts, figures, etc. In essence all members need to at least upload text to the platform, with figures and graphics, markup language and semantic annotations added or harmonized by specific groups. This is detailed in the deliverable specification.
  • And we will work on a joint publication describing this initiative. We will start this document once we have more concrete definitions/specifications of the deliverable.

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Week 010: 26/10/2022 to 02/11/2022

It has been 2.5 months since our first meeting, at the end of August. We took a very important step in starting this community resource and harmonization effort, drawing the general lines of what we want to achieve and sketching a plan on how to achieve it. We have since worked to add some more strokes to the sketch, studying models (infrastructure, work division, citation) that would fit with our vision and constraints. Tomorrow we will have the opportunity to discuss those in more detail.

We have also worked to make the broader community aware of this effort and to bring new members to the group, advertising it in meetings, sending direct invitations, and preparing the website. At the same time, we have structured ourselves further, with thematic areas and thematic area coordinators that volunteered to help organize the effort. Topic discussions have also started in our mailing list with interesting propositions and perspectives, and draft documents capturing those ideas. And we have gained important support from individuals/institutions with knowhow on the type of infrastructure we need to bring this project to life.

We have much to do, but I believe we are on a good track.

Updates:

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Week 009: 19/10/2022 to 26/10/2022

This week we welcome:

  • Barbara Bulgarelli from JRC (IT);
  • Chuanmin Hu from USF (US);
  • Rabia Khan from SYR (US);

Updates:

  • The final agenda for the second plenary meeting is available. The meeting takes place next week, November 3. We have adapted it considering the current material available from the thematic areas and added an important discussion on publication / citation models. Since we have many new members, we will also present an overview of this focus group;
  • We have started a draft with the list of entries organized by thematic area;
  • Our group has grown to over 50 members over the last two months, with a diversity of expertises and affiliations! We believe this diversity and scale are important for a community-driven resource, and for its actual adoption into our lexicon.

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Week 008: 12/10/2022 to 19/10/2022

This week we welcome:

  • Martin Ligi from UT (EE);

Updates:

  • As you now know from the calendar invitations we sent last week, we will have a presentation about the Semantic MediaWiki software as a potential alternative of infrastructure for this project. Semantic MediaWiki is a semantic web extension to the MediaWiki (software that runs Wikipedia). The meeting will take place on November 23.
  • We have updated the organogram;
  • And started a draft document on the roles within the NFG: roles.

Notes:

  • We are two weeks away from our next meeting and we are still needing to have some example entries from the thematic areas;
  • We are also needing to get the list of terms concepts that each thematic area will potentially curate.

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Week 007: 05/10/2022 to 12/10/2022

This week we welcome:

  • Agnieszka Bialek from NPL (UK);
  • Alexandre Corizzi from LOV (FR);
  • Samantha Lavender from Pixalytics (UK);

Updates:

  • We received a lot of positive feedback on the strategy for the invitation of co-coordination of the thematic areas. Most thematic areas have at least one coordinator, except biology, geology and Earth Observation. Any one of those groups willing to have at least for a time a coordination role?
  • At the FAR-2 workshop in Belgium we had some interesting discussions on nomenclature two, pointing out some problems with the concept of BRDF correction, when it is actually a hemispherical-directional (or conical) correction.
  • We got a representative of the Semantic MediaWiki o give a presentation for our group. It will be a presentation 23 or 24 of november. Soon we will send an invitation.
  • Alex Castagna started a draft for an entry of the optics thematic group wich is open for comments before presentation on our next meeting: glint.

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Week 006: 28/09/2022 to 05/10/2022

This week we welcome:

  • Abhishek Kumar from UMASS (US);
  • Deepak Mishra from UGA (US);
  • Hongyan Xi from AWI (DE);

Updates:

  • We have sent out invitation emails to selected members of each thematic area to act as coordinators. While we welcome all volunteers, for our invitations we have tried to follow the some guidelines: (1) invite two members of each thematic area to share the coordination; (2) have female and male leads; (3) combine early and senior career scientists; (4) cover geographical regions (funding, agencies, regional communities); (5) cover different niche expertises inside a given thematic area.
  • As suggested by Tristan, we have added a new thematic group: historical notes. The idea I believe would be to work adding historical perspectives to entries that do not have them yet or expand existing ones. It was added to our thematic areas file.
  • Ils Reusen has sent us the Water-ForCE glossary (V1) – it is now in our reference folder and an entry was added to our reference list.

Summaries:

  • Robert Frouin proposed to organize within the group a paper focused on the nomenclature for reflectance in hydrologic optics / aquatic remote sensing. This could be a great way to get us started.

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Week 005: 21/09/2022 to 28/09/2022

This week we welcome:

  • Guillaume Morin from INRAE (FR);

Updates:

  • The minutes from the first meeting we prepared by Daniela Gurlin last week. You are welcomed to read this document and to suggest addition or change of content.
  • We have also sent emails this morning to all thematic areas that do not have a coordinator with the goal of choosing coordinators and organizing the work in each thematic area. We have about one month until the next meeting and the more groups present example entries the better will be the results of the meeting.
  • Finally, we have invited the coordinator of the Semantic MediaWiki, a project that extends the MediaWiki (the software powering Wikipedia) with semantic web standards, to give a presentation to our group or to suggest another presenter. We are still waiting for a reply. Alex believes that the Semantic MediaWiki could be the best solution for cooperative content creation incorporating semantic web. Any other suggestions are welcomed.

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Week 004: 14/09/2022 to 21/09/2022

This week we welcome:

  • Emanuele Organelli from ISMAR (IT);
  • Jaime Pitarch from ISMAR (IT);
  • Thomas Jordan from PML (UK);

We will communicate with the subgroups of different thematic areas this week to select a coordinator.
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Week 003: 07/09/2022 to 14/09/2022

This week we welcome the new members:

  • Bozena Wojtasiewicz from CSIRO (AU);
  • Caren Binding from ECCC (CA);
  • Marco Talone from ICM-CSIC (ES);

Updates:

  • For the members that had not filled the thematic_areas_membership file, we have added their names to thematic areas they might be interested in as a suggestion – please do check and update the thematic area sheets accordingly. The coordination of each group will be defined by its members. Temporarily we have Curt on the optics group and Heidi in the benthic habitats group – they have volunteered to start the work and may continue as coordinators depending on their availability and group evolution.

Notes:

  • The coordinators (or me in case a group has no coordinator) will send a message to their group to start the work. A summary of what we want to achieve from the “content” part by the next meeting is:
  1. thematic area groups formed and organized;
  2. a comprehensive list of the entries that will be curated by each group;
  3. and a definition of the format of those entries.

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Week 002: 31/08/2022 to 07/09/2022

This week we welcome to the team:

  • Griet Neukermans from UGent (BE).
  • Ian Carroll from NASA (US);

Updates:

  • Thank you for joining the meeting last week. Daniela took several notes and will soon upload the minute to the meeting folder (which you can amend if necessary). Here I will just point out major conclusions of meeting:
  1. The organization of the nomenclature group was established to be a general coordination occupied by Alexandre Castagna and Daniela Gurlin, thematic groups coordinations and collective of volunteers:
    gaw_nfg_organogram;
  2. The number a subject of the thematic groups (and their scope) will be defined by the members. Each group will self-organize (e.g., choose its coordinator). A document was created to contain the group areas, members, coordinators and scopes: thematic_areas_membership
  3. Each group will produce about 2 examples of entries and those will serve as basis for a discussion to define the template / style / structure of the entries. We have created a poll to set the next meeting date. It will be send in a separate e-mail.
  4. The broad strokes of the deliverable were defined and compiled in the following document: deliverables_key_points

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Week 001: 24/08/2022 to 31/09/2022

This week we welcome to the team:

  • Áurea Ciotti from USP (BR);
  • Christopher Proctor from NASA (US);
  • Claudia Giardino from IREA-CNR (IT);
  • Colleen Mouw from URI (US);
  • Collin Roesler from Bowdoin College (US);
  • Curtis Mobley (US);
  • Heidi Dierssen from UCONN (US);
  • Ils Reusen from VITO (BE);
  • Ken Voss from UMiami (US);
  • Nima Pahlevan from NASA (US);
  • Olivier Burggraaff from ULeiden (NL);
  • Peter Gege from DLR (DE);
  • Robert Frouin from UCSD (US);
  • Sara Calle from UGA (US);
  • Stella Berger from IGB (DE);
  • Steven Greb from WINSC (US);
  • Susanne Craig from NASA (US);
  • Tristan Harmel from Magellium (FR);
  • Vittorio Brando from CNR (IT);
  • Xiaodong Zhang from USM (US);
  • Zhongping Lee from UMASS (US);

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Week 000: Foundation during the ESA Living Planet Symposium 2022

The Nomenclature Focus Group was born out of a group discussion on terminology in hydrologic optics and aquatic remote sensing during the ESA Living Planet Symposium 2022. The members of the discussion were interested in forming an initiative to solve some of the identified issues and GEO AquaWatch offered to host this effort. Initial members:

  • Alexandre Castagna from UGent (BE);
  • Arnold Dekker from Satdek (AU);
  • Dalin Jiang from UStirling (UK);
  • Daniela Gurlin (DE);
  • Evangelos Spyrakos UStirling (UK);
  • Igor Ogashawara from IGB (DE);
  • Jens Nejstgaard from IGB (DE);
  • Marit Oostende from Helmholtz-Zentrum Hereon (DE);
  • Merrie Beth Neely from USF (US);
  • Mortimer Werther from UStirling (UK);
  • Shun Bi from Helmholtz-Zentrum Hereon (DE).
Creation of the GEO AquaWatch Nomenclature Focus Group. May 2022.

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