Creating RESTful APIs over SPARQL endpoints using RAMOSE

Semantic Web technologies are widely used for storing RDF data and making them available on the Web through SPARQL endpoints, queryable using the SPARQL query language. While the use of SPARQL endpoints is strongly supported by Semantic Web experts, it hinders broader use of RDF data by common Web users, engineers and developers unfamiliar with Semantic Web technologies, who normally rely on Web RESTful APIs for querying Web-available data and creating applications over them. To solve this problem, we have developed RAMOSE, a generic tool developed in Python to create REST APIs over SPARQL endpoints. Through the creation of source-specific textual configuration files, RAMOSE enables the querying of SPARQL endpoints via simple Web RESTful API calls that return either JSON or CSV-formatted data, thus hiding all the intrinsic complexities of SPARQL and RDF from common Web users. We provide evidence that the use of RAMOSE to provide REST API access to RDF data within OpenCitations triplestores is beneficial in terms of the number of queries made by external users of such RDF data using the RAMOSE API, compared with the direct access via the SPARQL endpoint. Our findings show the importance for suppliers of RDF data of having an alternative API access service, which enables its use by those with no (or little) experience in Semantic Web technologies and the SPARQL query language. RAMOSE can be used both to query any SPARQL endpoint and to query any other Web API, and thus it represents an easy generic technical solution for service providers who wish to create an API service to access Linked Data stored as RDF in a triplestore.

Serving IIIF and DTS APIs specifications from TEI data via XQuery with support from a SPARQL Endpoint

This paper presents two modules, one serving the IIIF presentation API, and another the three Distributed Text Services API specifications (Collection, Navigation and Document), as well as an additional experimental Web Annotation and indexes API. These are all served from XML TEI data with a RESTxq XQuery module within an exist-db application which also benefits from direct access to a SPARQL Endpoint containing a serialization in RDF of some of the information in the XML. The setup is not uncommon: we have our data collaboratively edited in GitHub, indexed from there into exist-db and transformed with XSLT to RDF-XML. The RDF-XML is passed on to a Apache Jena Fuseki on the same server and is indexed there as well, as RDF so that the two datasets are parallel and updated synchronously. What I want to argue is that the setup itself and the code involved are integrating part of the knowledge being served. They make assumption on the existing data and build the additional representation using that with an additional set of inferences. I conclude the contribution with some examples of use of these modules and their functions.

IDSM ChemWebRDF: SPARQLing small-molecule datasets

The Resource Description Framework (RDF), together with well-defined ontologies, significantly increases data interoperability and usability. The SPARQL query language was introduced to retrieve requested RDF data and to explore links between them. Among other useful features, SPARQL supports federated queries that combine multiple independent data source endpoints. This allows users to obtain insights that are not possible using only a single data source. Owing to all of these useful features, many biological and chemical databases present their data in RDF, and support SPARQL querying. In our project, we primary focused on PubChem, ChEMBL and ChEBI small-molecule datasets. These datasets are already being exported to RDF by their creators. However, none of them has an official and currently supported SPARQL endpoint. This omission makes it difficult to construct complex or federated queries that could access all of the datasets, thus underutilising the main advantage of the availability of RDF data. Our goal is to address this gap by integrating the datasets into one database called the Integrated Database of Small Molecules (IDSM) that will be accessible through a SPARQL endpoint. Beyond that, we will also focus on increasing mutual interoperability of the datasets. To realise the endpoint, we decided to implement an in-house developed SPARQL engine based on the PostgreSQL relational database for data storage. In our approach, data are stored in the traditional relational form, and the SPARQL engine translates incoming SPARQL queries into equivalent SQL queries. An important feature of the engine is that it optimises the resulting SQL queries. Together with optimisations performed by PostgreSQL, this allows efficient evaluations of SPARQL queries. The endpoint provides not only querying in the dataset, but also the compound substructure and similarity search supported by our Sachem project. Although the endpoint is accessible from an internet browser, it is mainly intended to be used for programmatic access by other services, for example as a part of federated queries. For regular users, we offer a rich web application called ChemWebRDF using the endpoint. The application is publicly available at https://idsm.elixir-czech.cz/chemweb/.

The ICOS Carbon Portal as example of a FAIR community data repository supporting scientific workflows

<p>The Integrated Carbon Observation System (ICOS) provides long term, high quality observations that follow (and cooperatively set) the global standards for the best possible quality data on the atmospheric composition for greenhouse gases (GHG), greenhouse gas exchange fluxes measured by eddy covariance and CO<sub>2</sub> partial pressure at water surfaces. The ICOS observational data feeds into a wide area of science that covers for example plant physiology, agriculture, biology, ecology, energy & fuels, forestry, hydrology, (micro)meteorology, environmental, oceanography, geochemistry, physical geography, remote sensing, earth-, climate-, soil- science and combinations of these in multi-disciplinary projects.<br>As ICOS is committed to provide all data and methods in an open and transparent way as free data, a dedicated system is needed to secure the long term archiving and availability of the data together with the descriptive metadata that belongs to the data and is needed to find, identify, understand and properly use the data, also in the far future, following the FAIR data principles. An added requirement is that the full data lifecycle should be completely reproducible to enable full trust in the observations and the derived data products.</p><p>In this presentation we will introduce the ICOS operational data repository named ICOS Carbon Portal that is based on the linked open data approach. All metadata is modelled in an ontology coded in OWL and based on a RDF triple store that is available through an open SparQL endpoint. The repository supports versioning, collections and models provenance through a simplified Prov-O ontology. All data objects are ingested under strict control for the identified data types on provision of the correct and sufficient (provenance) metadata, data format and data integrity. All data, including raw data, is stored in the long term trusted repository  B2SAFE with two replicates. On top of the triple store and SparQL endpoint we have built a series of services, APIs and graphical interfaces that allow machines to machine and user interaction with the data and metadata. Examples are a full faceted search with connected data cart and download facility, preview of higher level data products (time series of  point observations and spatial data), and cloud computing services like eddy covariance data processing and on demand atmospheric footprint calculations, all connected to the observational data from ICOS.  Another interesting development is the community support for scientific workflows using Jupyter notebook services that connect to our repository through a dedicated python library for direct metadata and data access.</p>

Dal Catalogo generale dei beni culturali al knowledge graph del patrimonio culturale italiano: il progetto ArCo

Le attività dell’ICCD sono da sempre indirizzate ad una maggiore condivisione e valorizzazione sia dei modelli di strutturazione della conoscenza sul patrimonio culturale sia dei dati prodotti nelle campagne di catalogazione. Negli ultimi anni l’ICCD ha concentrato le proprie attività sull’analisi e sull’applicazione delle potenzialità offerte dal semantic web e dai suoi strumenti. Uno dei risultati è il progetto ArCo, il grafo della conoscenza del patrimonio culturale italiano, costituito da una rete di ontologie e da oltre 169 milioni di triple riferite a oltre a 800 mila schede catalografiche. ArCo si basa sui dati del Catalogo generale dei beni culturali dell’Istituto centrale per il catalogo e la documentazione del MiBACT e sui dati dei suoi archivi fotografici. ArCo è distribuito congiuntamente con uno SPARQL endpoint, un software per convertire i record di catalogo in RDF e una ricca suite di materiale di documentazione (test, valutazione, istruzioni, esempi ecc.).

MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models

MetaNetX/MNXref is a reconciliation of metabolites and biochemical reactions providing cross-links between major public biochemistry and Genome-Scale Metabolic Network (GSMN) databases. The new release brings several improvements with respect to the quality of the reconciliation, with particular attention dedicated to preserving the intrinsic properties of GSMN models. The MetaNetX website (https://www.metanetx.org/) provides access to the full database and online services. A major improvement is for mapping of user-provided GSMNs to MXNref, which now provides diagnostic messages about model content. In addition to the website and flat files, the resource can now be accessed through a SPARQL endpoint (https://rdf.metanetx.org).

Visualisasi Pemain Sepak Bola Indonesia pada DBPedia dengan menggunakan Node2Vec dan Closeness Centrality

Visualization of Indonesian Football Players on DBpedia through Node2Vec and Closeness Centrality Implementation. Through Semantic Web, data available on the internet are connected in a large graph. Those data are still raw so that they need to be processed to be an information that can help humans. This research aims to process and analyze the Indonesian soccer player graph by implementing node2vec and closeness centrality algorithm. The graph is modeled through a dataset obtained from the DBpedia by performing a SPARQL query on the SPARQL endpoint. The results of the Node2vec algorithm and closeness centrality are visualized for further analysis. Visualization of node2vec shows that the defenders are distributed over the players. Meanwhile, the result of closeness centrality shows that the strikers have the highest centrality score compared to other positions.Keywords: visualization, node2vec, closeness centralityAbstrak. Dengan adanya web semantik, data yang tersebar di internet dapat saling terhubung dan membentuk suatu graf. Data yang ada pada graf tersebut masih berupa data mentah sehingga perlu dilakukan pengolahan agar data mentah tersebut dapat menjadi informasi yang dapat membantu manusia. Penelitian ini bertujuan untuk melakukan pengolahan dan analisis terhadap graf pemain sepak bola Indonesia dengan mengimplementasikan algoritma node2vec dan closeness centrality. Graf dimodelkan melalui dataset yang didapat dari website DBpedia dengan cara melakukan query SPARQL pada SPARQL endpoint. Hasil dari algoritma node2vec dan closeness centrality divisualisasikan untuk dianalisis. Visualisasi dari node2vec menunjukkan pemain defender tersebar. Hasil closeness centrality menunjukkan bahwa pemain striker memiliki nilai tertinggi daripada posisi lainnya.Kata Kunci: visualisasi, node2vec, closeness centrality

BiGe-Onto: An ontology-based system for managing biodiversity and biogeography data1

Great progress to digitize the world’s available Biodiversity and Biogeography data have been made recently, but managing data from many different providers and research domains still remains a challenge. A review of the current landscape of metadata standards and ontologies in Biodiversity sciences suggests that existing standards, such as the Darwin Core terminology, are inadequate for describing Biodiversity data in a semantically meaningful and computationally useful way. As a contribution to fill this gap, we present an ontology-based system, called BiGe-Onto, designed to manage data together from Biodiversity and Biogeography. As data sources, we use two internationally recognized repositories: the Global Biodiversity Information Facility (GBIF) and the Ocean Biogeographic Information System (OBIS). BiGe-Onto system is composed of (i) BiGe-Onto Architecture (ii) a conceptual model called BiGe-Onto specified in OntoUML, (iii) an operational version of BiGe-Onto encoded in OWL 2, and (iv) an integrated dataset for its exploitation through a SPARQL endpoint. We will show use cases that allow researchers to answer questions that manage information from both domains.