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Workshop: Ontologies4Chem

The first Ontologies4Chem Workshop organised by NFDI4Chem took place on September 7th – 8th 2022 as an online event with over 50 international participants. The overarching aim of the workshop was to bring together experts from various ontology projects with domain/ontology experts, software developers and service providers from NFDI4Chem and other NFDI consortia related to chemistry. After a brief introduction of NFDI4Chem and our previous work on identifying ontologies relevant to the NFDI4Chem context, the focus of the first day of the workshop was on reports and discussion of the current state and future plans of most of the relevant chemistry ontologies (CHEMINF, Chebi, ChIRO, EDAM, CHEMROF, OBI, SIO, CHMO, RXNO, MOP) presented by their curators. The presentation of the ontologies was complemented by the IUPAC Gold Book as definition source. As an additional perspective, NFDI4Cat and NFDI4Health presented their plans and application of ontologies. The first day closed with an update on tools like ROBOT, NFDI4Chem Terminology Service and ODK, used for developing and working with ontologies. The second day of the workshop was focused on exchanging experiences and discussing best practices in ontology development and curation as well as on data annotation using ontologies. It began with previous work done in NFDI4Chem towards Raman & NMR spectroscopy and future developments for the Terminology Service, followed by ontology development workflows in NFDI4Cat, extending Bioschemas.org towards chemistry, the IUPAC FairSpec project, the application of ontologies in Pubchem and ClassyFire framework. The day ended with two parallel breakout sessions for deeper discussions and hands-on demonstrations on data annotations and ontology curation.

The most important outcome of the workshop was a wide agreement on working closer together with the involved communities to improve the quality of existing chemical ontologies, as well as on engaging more domain experts in the field. A mailing list and a dedicated chemistry channel in the OBO Slack were launched to stay in touch and plan the next steps.

There will be a second Ontologies4Chem Workshop in 2023! 

Further links:
Slides of the presentations are available from the workshop agenda and joint notes.
Recordings of the presentations are available on NFDI4Chem YouTube channel

Ontologies4Chem: The Landscape of Ontologies in Chemistry Published

Why are ontologies an essential building block not only for NFDI4Chem, but all NFDI?

FAIR data is all about human AND machine-readable data. Ontologies are used to semantically describe data, information and knowledge in a domain. Terms, relationships, and logic described in an ontology enable us to semantically annotate and link data to create knowledge graphs. Quite a few chemical ontologies already exist to describe molecules, reactions, the role of molecules in reactions and analytical procedures. These semantic descriptions take data to the next level, making them machine-understandable.

To address the application of ontologies in research data management we recently published an overview of ontologies in chemistry suitable to represent concepts of research and research data in Pure and Applied Chemistry. The reviewed ontologies were evaluated against several criteria derived from the FAIR data principles and their possible application in the digitisation of RDM workflows. To summarise our criteria shortly; to be included an ontology had to be made by domain experts, published and maintained in a FAIR way, being actively and openly maintained as well as being used in established applications.

Read more: P. Strömert, J. Hunold, A. Castro, S. Neumann, O. Koepler, Ontologies4Chem: the landscape of ontologies in chemistry, Pure Appl. Chem. 2022, doi: 10.1515/pac-2021-2007.

Ontologies4Chem Workshop

September 7 & 8, 2022, 14.00 – 18.00 CEST, Online

Ontologies are a cornerstone of FAIR machine-readable data. They provide terms, relations and logic to semantically annotate and link research data building knowledge graphs. Integrating ontologies into electronic lab notebooks, data repositories and software tools enables users to create rich annotated data from the very beginning. In the past, several ontologies with relation to the chemistry domain have been developed. In Task Area 6 Synergies we evaluate the application of these ontologies for research data management, identify gaps and initiate the development of missing ontologies.

To our first Ontologies4Chem Workshop we invite ontology curators, ontology engineers, software and data repository developers and domain experts currently applying ontologies or with an interest to do so in the future.

Aims of the workshop are:

  • Deepen and/or establish collaboration between ontology curators and NFDI4Chem + other NFDI consortia related to chemistry
  • Develop joint strategies: ontologies for research data management and beyond
  • Application of ontologies in research data annotations
  • Inspire service developers and data repository developers to use ontologies
  • Inspire chemists to use ontologies
  • Work concretely on ontologies

The first day will offer flash talks about current and future developments on ontologies and ontology tools. The second day will be all about best practice and two hands-on sessions on ontology curation and data annotation using ontologies.

Registration is open now.

Scientific Software Engineer / Ontology Engineer (m/f/d)

The National Research Data Infrastructure (NFDI) is an outstanding infrastructure initiative for the science communities in Germany with the aim to harness the great potential of Research Data as a valuable resource for science and research. Since 1st October 2020, the first round of NFDI consortia receives funding for a period of five years, with the option of a five-year extension.

Within this network, the Technische Informationsbibliothek (TIB) – Leibniz Information Centre for Science and Technology – Program Area C, Research and Development, is looking to employ a

Scientific Software Engineer / Ontology Engineer (m/f/d)

to join the Lab Linked Scientific Knowledge at the earliest possible opportunity.

The position initially limited to 2 years with envisioned extension. The regular weekly working time is 39.8 hours (full-time). The position is only suitable for part-time work to a limited extent. The remuneration is based up to pay scale group 13 TV-L, depending on the successful applicant’s qualifications and depending on the assigned tasks and responsibilities.

Your challenge
The Lab Linked Scientific Knowledge develops tools and methodologies to support scientists in the digitization of their research. This includes tools to document research activities and the acquisition, processing, analysis, storage, publication and re-use of research data.

Your tasks will be the development of knowledge management systems and tools for semantic annotation of data using ontologies. Other duties will include converting data to RDF as well as storage, retrieval, and visualization. We expect you to be able to independently install, run, and maintain necessary software to build semantically annotated data repositories. This requires solid knowledge of virtualization platforms such as Docker as well as databases such as Virtuoso, Apache Jena, MongoDB and others.

With your work in an interdisciplinary team, you will make an important contribution to information infrastructure projects of Collaborative Research Centers from the engineering sciences as well as NFDI4Chem, the Chemistry Consortium in the National Research Data Infrastructure (NFDI).

Your tasks will focus on

  • Development, curation, and integration of ontologies for chemistry and engineering.
  • Development of controlled vocabularies and classifications to standardize data for research data management (RDM).
  • Development of semantic tools for handling ontologies and semantification of research data.
  • Development of knowledge management systems in the context of information infrastructure projects of collaborative research centres from engineering sciences.
  • Community outreach and joint development and curation of ontologies with domain experts and ontology users.
  • Organization of ontology workshops for and with the scientific community.

Your qualities
The successful candidate will have experience in computer science, chemistry or engineering sciences. You are familiar with controlled vocabularies and ontologies to describe domain concepts. Excellent verbal and written communication skills are essential in order to collaboratively develop ontologies together with the scientific community during workshops and discussions. You should be able to think creatively, grasp new knowledge quickly, and be interested in innovative software systems and in mastering complex challenges.

Requirements

  • Completed university degree (Bachelor’s or Master’s degree) in a relevant field of study such as computer science, engineering sciences, chemical informatics, bioinformatics, information sciences or comparable.
  • Excellent knowledge of modern programming languages (especially Python, Java, PHP as well as JavaScript and HTML) and modern software development methods.
  • Proven skills in software development in a team.
  • Experience in developing, integrating and publishing controlled vocabularies, terminologies and ontologies
  • Knowledge in ontology development and with core semantic technologies (RDF, OWL, SPARQL).
  • Solid experience in using RDF and SPARQL for data modeling and querying.
  • Experience in knowledge representation and logic, semantic technologies, and web engineering.
  • Knowledge and hands-on experience with ontology tools such as Protegé, WebProtegé or WebVOWL.
  • Excellent verbal and written communication skills.

The following will be considered an advantage

  • Experience with WikiMedia software environments, especially Semantic MediaWiki.
  • Proficiency in the German language.
  • Experience with CI/CD workflows in GitLab.
  • Experience in DevOps and/or system administration.
  • Familiarity with and interest in scientific data and metadata management.
  • Knowledge of tools and services for research data management.

What we offer
Our mission is to keep rethinking and innovating the provision and use of research data and information. In TIB’s Research and Development Department, you have the opportunity to advance your career in a sizable, dynamic and excellent environment. We provide a scientifically and intellectually inspiring environment with an entrepreneurial mindset embedded in a leading technical university and one of the largest technical information centres being part of the Leibniz Association. TIB collaborates closely with the L3S Research Centre at Leibniz University Hannover, one of the world’s leading research institutes in the field of Web & Data Science, within the Leibniz Joint Lab Data Science & Open Knowledge. Last but not least, we attach great importance to an open, creative and fun work atmosphere.

Furthermore, we offer

  • Financing for necessary equipment, conference and research visit travel.
  • Work in the context of national and international research and innovation projects.
  • A portfolio of technology components, including ORKGOpenResearch.orgTIB AV-PortalDBpedia.org, among others.
  • A modern workplace in a central location of Hanover with a collegial, attractive and versatile working environment.
  • A comprehensive and in-depth training.
  • Flexible working hours (flexitime) as well as offers for reconciling work and family life such as mobile work and remote work options.
  • An employer with a wide range of internal and external further education and training measures, workplace health promotion and a supplementary pension scheme for the public sector (VBL).
  • Discount for employees in the canteens of the Studentenwerk Hannover as well as the possibility to use the various offers of the University Sports Hannover.
  • A job in the public service oriented towards the common good with a salary in pay scale group 13 TV-L according to the provisions of the collective agreement for the public service in Germany (TV-L), including a special annual payment and 30 days of vacation per year.

Questions regarding the content of the position can be addressed to Dr. Oliver Koepler, head of Lab Linked Scientific Knowledge, by mail at oliver.koepler@tib.eu

How to apply
We look forward to receiving your application.

Paper applications are also possible on an equal basis. In this case, please send your complete application documents with the subject 36/2022 before July 14, 2022 addressed to

Technische Informationsbibliothek (TIB)
Personalservice
Herrn Daniel Eilers
Welfengarten 1 B
30167 Hannover
Germany

or alternatively as a single PDF document file to bewerbungtibeu. For applications in digital from, please send a PDF file with a maximum size of 10 MB.

In the case of foreign university degrees, it is mandatory to submit a Statement of Comparability from the Central Office for Foreign Education (ZAB) for the final assessment of the hiring requirements during the hiring process (link for more information). A fee will be charged for this. This obligation does not apply if the foreign university degree has already been assessed by an expert and is listed in the ANABIN database of the ZAB as an equivalent university degree (link to ANABIN database).

Who we are
TIB, being part of the Leibniz Research Association, is with around 600 employees one of the largest technical information centres in Germany, having three main functions:

  1. Acting in the capacity of the Leibniz Information Centre for Science and Technology, our forward-looking services secure the infrastructural requirements for providing researchers in science and industry with high-quality information and literature.
  2. Carrying out cutting edge research to further expand TIB’s role as a German information centre for the digitisation of science and technology.
  3. Offer library services for the Leibniz University Hannover.

TIB is an equal opportunity employer, providing ideal working conditions, and continuously taking action to enable its employees to combine career interests with family life.

Severely disabled candidates with comparable qualifications will be given preferential treatment. We welcome applications from all nationalities.

Please note that your application documents will not be returned and application and travel costs cannot be reimbursed.

Please indicate in the subject line of your application through which job board you became aware of our offer.

Software Developer / Semantic MediaWiki specialist (m/f/d)

The National Research Data Infrastructure (NFDI) is an outstanding infrastructure initiative for the science communities in Germany with the aim to harness the great potential of Research Data as a valuable resource for science and research. As of 1st October 2020, the first round of NFDI consortia receives funding for a period of five years, with the option of a five-year extension. TIB plays a key role in shaping the NFDI from the very beginning.

Within this network, the Technische Informationsbibliothek (TIB) – Leibniz Information Centre for Science and Technology – Program Area C, Research and Development, is looking to employ a

Software Developer / Semantic MediaWiki specialist (m/f/d)

to join the Lab Linked Scientific Knowledge at the earliest possible opportunity.

The position is initially limited to 3 years, but further employment is intended. The regular weekly working time is 39.8 hours (full-time). The position is only suitable for part-time work to a limited extend. The remuneration is based up to pay scale group 13 TV-L, depending on the applicant’s qualifications and depending on the assigned tasks and responsibilities.

Your tasks

Your tasks will be the co-design of knowledge management systems for information infrastructure projects of collaborative research centres and the development of tools for semantic data annotation and cross-domain mapping of ontologies as well as the provision of terminology services for NFDI4Chem, the chemistry consortium in the National Research Data Infrastructure. Your tasks will be embedded in an interdisciplinary team

Possible areas of work include, but are not limited to

  • Implementation, development and maintenance of the software MediaWiki, Semantic MediaWiki and their extensions
  • Development of SMW-based knowledge management systems in the context of information infrastructure projects of special research areas from engineering sciences
  • Contributing to the development and curation of controlled vocabularies and ontologies for describing data for research data management (RDM) in chemistry
  • Development of semantic tools for handling ontologies and semantification of data in chemistry 

Your qualities

  • Completed university degree (Bachelor’s or Master’s degree) in a relevant field of study such as computer science, engineering sciences, chemical informatics, bioinformatics, information sciences or comparable
  • Experience with working in an agile software development environment, particularly with web-based applications
  • Experience with WikiMedia software environments, especially Semantic MediaWiki
  • Very good knowledge in one or more of the following programming languages: Python, JavaScript and PHP
  • Experience with core semantic web technologies (OWL, RDF, SPARQL)
  • Experience with version management systems based on Git
  • High degree of self-organisation and ability to work independently
  • Very good written and spoken English skills; proficiency in German is a plus
  • Willingness to learn new technologies and languages

Desired additions to your profile

  • Experience with Research Data Management in Engineering Sciences or Chemistry
  • Interest in working in a research and library environment
  • Willingness to be engaged with other scientific disciplines
  • Experience with CI/CD workflows based on GitLab
  • Experience in DevOps and/or system administration

What we offer

The Lab Linked Scientific Knowledge is part of the Data Science & Digital Libraries Research Group. TIB’s Research and Development Department offers a scientifically and intellectually inspiring environment with an entrepreneurial mindset, embedded in a leading technical university and one of the largest technical information centres being part of the Leibniz Association.

The research department at the TIB is relatively young and offers many opportunities. It is our vision to rethink the representation and provision of data and information and to organize them in an Open Research Knowledge Graph (ORKG) in the future. There is a close cooperation with the L3S Research Centre at Leibniz University Hannover, one of the world’s leading research institutes in the field of Web & Data Science, within the Leibniz Joint Lab Data Science & Open Knowledge.

Last but not least, we attach great importance to an open and creative working atmosphere in which it is fun to work.

Furthermore, we offer

  • Funding for necessary equipment, conference and research visit travel
  • Work in the context of a national research and innovation projects
  • A portfolio of technology components to build on, including ORKGOpenResearch.orgTIB AV-PortalDBpedia.org and other
  • A modern workplace in a central location of Hanover with a collegial, attractive and versatile working environment
  • Flexible working hours (flexitime) as well as offers for reconciling work and family life such as mobile work and remote work options
  • An employer with a wide range of internal and external further education and training measures, workplace health promotion and a supplementary pension scheme for the public sector (VBL)
  • Discount for employees in the canteens of the Studentenwerk Hannover as well as the possibility to use the various offers of the University Sports Hannover
  • A job in the public service with a salary up to pay scale group 13 TV-L according to the provisions of the collective agreement for the public service in Germany (TV-L), including a special annual payment and 30 days of vacation per year

If you are interested, questions regarding the position can be addressed to Dr. Oliver Koepler, head of the Lab Linked Scientific Knowledge, by e-mail at Oliver.Koeplertibeu.

How to apply
We look forward to receiving your application.

Paper applications are also possible on an equal basis. In this case, please send your complete application documents with the subject 12/2022 before March 24th 2022 addressed to

Technische Informationsbibliothek (TIB)
Personalservice
Herrn Daniel Eilers
Welfengarten 1 B
30167 Hannover
Germany

or alternatively as a single PDF document file to Bewerbung (at) tib.eu. For applications in digital from, please send a PDF file with a maximum size of 10 MB.

Who we are
TIB, being part of the Leibniz Research Association, is with around 550 employees one of the largest technical information centres in Germany, having three main functions:

  1. Acting in the capacity of the Leibniz Information Centre for Science and Technology, our forward-looking services secure the infrastructural requirements for providing researchers in science and industry with high-quality information and literature.
  2. Carrying out cutting edge research to further expand TIB’s role as a German information centre for the digitisation of science and technology
  3. Offer library services for the Leibniz University Hannover.

TIB is an equal opportunity employer, providing ideal working conditions, and continuously taking action to enable its employees to combine career interests with family life. It wants to promote equal career opportunities for women and men in particular and therefore urges qualified women to apply.

Severely disabled candidates with comparable qualifications will be given preferential treatment.

We welcome applications from all nationalities.

Please indicate in the subject of your application which job exchange brought our offer to your attention.

Please note that your application documents will not be returned, and application and travel costs cannot be reimbursed.

.

Event Throwback: Minimum Information Standards, NFDI4Chem Takes the International Stage – Part I

Efforts for the development of minimum information standards for research data in chemistry have to be addressed in an international context. Thus, Dr. Johannes Hunold (TIB) presented NFDI4Chem’s vision for terminologies and semantic annotation of research data in the “Gold Book project session” dedicated to the IUPAC Compendium of Chemical Terminology (informally known as “Gold Book”) at the 51st IUPAC General Assembly, from August 9-15. In his talk Dr. Hunold outlined the impact and interdependence of the current development of chemistry terminologies and a terminology service by NFDI4Chem on the latest activities around the Gold Book. Participants of the session thoroughly discussed the results of the “Backup, Maintenance, and Redevelopment of the IUPAC Gold Book website” project and the next steps toward further semantification of the Gold Book and its role in the context of ontology development (see project “Development of an IUPAC Recommended Term Management System for Expansion of the Coverage of the IUPAC Compendium on Chemical Terminology“). The participants agreed that the Gold Book should continue to serve as a “source of truth” and uniform standard for the definition of relevant terms in the field of chemistry to be reused in chemistry ontologies whenever possible.

It was agreed that terminologies in particular play an important role in the implementation of the FAIR data principles and a sustainable RDM. The editing and semantic annotation of research data will be an elementary part of the everyday research process in the future. This will lay the foundation for machine-readable data and the application of methods such as machine learning.

Long-term, well-funded and community-driven infrastructure projects such as NFDI4Chem are important key players to support IUPACs mission in the implementation process of chemical standards in the digital domain.

With Prof. Dr. Christoph Steinbeck joining the CPCDS committee (Committee on Publications and Cheminformatics Data Standards) in January 2022, the NFDI4Chem consortium will be able to contribute even more directly to the standardisation of research data management in the field of chemistry.

NFDI4Chem Terminology Service Launched

NFDI4Chem proudly announces the launch of its Terminology Service for the Chemistry community. 

What is it good for, you ask?

As you probably know, the FAIR data principles play a key role in the development of the NFDI. Specifically, one  of the principles calls  for rich metadata describing data by using a formal, accessible, shared, and broadly applicable language for knowledge representation. The ambiguity of natural language words and phrases used to annotate data with their meaning has been a major obstacle so far. Here we can achieve a significant improvement through the application of domain-specific terminologies which allows us to unambiguously annotate data semantically. Standardised vocabularies mapped across the various disciplines enable real data interoperability, discovery and exploitation beyond our own domain.

Our Terminology Service provides such chemistry specific terminologies or ontologies. This enables researchers, software tools and services of NFDI4Chem to create machine- and human-readable descriptions of research data.

The first release of the Terminology Service facilitates exploration and browsing of existing ontologies in chemistry. You can search for terms and their usage in the different ontologies. Additionally, you can view ontology statistics and associated descriptive metadata or download ontology files. Various visualisation options are available to explore an ontology and the relations of terms. The curation function supports the suggestion of new ontologies or the recommendation of missing terms to the curator.

The Terminology Services further provides an extensive API to be used by other services and software tools. One example is the integration of terminologies when using the chemotion ELN to annotate experimental descriptions with terms of name reactions in organic chemistry from the RXNO ontology. RXNO provides a controlled vocabulary to unambiguously describe applied reactions. The encoded semantics, logic and taxonomy of reaction classes enable semantic queries on annotated data in the future. In the same way data repositories can use the Terminology Service to support the semantic annotation of research data during the upload process.

In the future this approach will enable interoperability of heterogeneous databases and cross-database semantic search. This will allow to overcome the limitation of keyword based searches moving to a search using the meaning of a keyword instead. 

The first release of the Terminology Service provides 18 ontologies identified to be useful for NFDI4Chem. It will be further developed in the future to include more ontologies, extended features, and linking tools for ontology curation and design.

If you have suggestions for terminologies / ontologies to be added or are interested in joining NFDI4Chem ontology activities, please contact helpdesk@nfdi4chem.de

The Terminology Service is developed and maintained by TIB – Leibniz Information Centre for Science and Technology. As one of the infrastructure partners within NFID4Chem TIB leads the activities of Task Area 6 – Synergies.

NFDI4Chem statement on Cross-Cutting Topics

The NFDI offers the opportunity to establish a science-driven, open, and high-quality national research data infrastructure. In August 2019, members of 11 consortia met to discuss common challenges posed by envisioned interoperability and data sharing across disciplines. As an important structural element for sustainable functionality of the NFDI, Cross-Cutting  Topics and their joint elaboration have been identified. As a first result 21 consortia agreed on a common list of cross-cutting topics, published in the Berlin declaration.

Since then, a number of initiatives have developed which address central issues of infrastructure development and in this way aim to support the discipline-oriented consortia in setting up the NFDI.

In February 2020, members of 14 consortia and 7 cross-cutting initiatives therefore met to discuss opportunities and challenges for a joint development of a national research data infrastructure.

NFDI4Chem welcomes and supports collaborative development of the Cross-Cutting Topics. We have therefore decided in agreement with the DFG to publish the chapter „The Consortium within the NFDI“ on the Cross-Cutting Topics describing our ideas and approach from the NFDI4Chem proposal as a contribution to an open and joint discussion of Cross-Cutting Topics. We hope that other consortia will follow suit and that we can jointly push forward the development of this important structural element of the NFDI.

You can download the PDF from our Downloads page.

Materials and Engineering / Chemistry Colloquium

On 17. and 18.12.2019, we defended the NFDI4Chem proposal at DFG Head Office, Bonn before an international panel of reviewers, representatives of NFDI expert panel and members of the DFG.

In a stimulating atmosphere we discussed questions of the experts on the strategy and proposed work plan of NFDI4Chem.

NFDI4Chem team at DFG Head Office, Oliver Koepler (TIB), Christoph Steinbeck (Uni Jena), Sonja Herres-Pawlis (RWTH Aachen), Matthias Razum (FIZ Karlsruhe), Nicole Jung (KIT)

We are looking forward to the review results, which will be send out in January 2020.  We will then given an opportunity to respond until February 2020. The final decision for funding will be made on 26 june, 2020.