The v2. You can add these plug-ins or get a current listing from the built-in updating mechanism ontopia is a relative complete suite of tools for building, maintaining, and deploying Topic Maps-based applications; open source, and written in Java.
In addition to the common ontology editing operations, it enables annotation of both ontology components and ontology changes. It supports the searching and filtering of user annotations, also known as notes, based on different criteria. Fully compliant with W3C standards, Composer offers comprehensive support for developing, managing and testing configurations of knowledge models and their instance knowledge bases. It is based on the Eclipse IDE.
It also contains an editor and a publishing system, and has support for automatic classification. There is also a web-based topic maps browser, and graphical visualization. Not Apparently in Active Use Adaptiva is a user-centred ontology building environment, based on using multiple strategies to construct an ontology, minimising user input by using adaptive information extraction Exteca is an ontology-based technology written in Java for high-quality knowledge management and document categorisation, including entity extraction.
Though code is still available, no updates have been provided since It includes a comprehensive tool suite allowing easy ontology creation and management and provides a framework for building ontology-based applications.
An important focus of KAON is scalable and efficient reasoning with ontologies Ontolingua provides a distributed collaborative environment to browse, create, edit, modify, and use ontologies. The server supports over active users, some of whom have provided us with descriptions of their projects. Provided as an online service; software availability not known. Applicable to webpages, text files and any input text in several languages BooWa is a set expander for any language formerly known as SEALS ; developed by RC Wang of Carnegie Mellon Google Keywords allows you to enter a few descriptive words or phrases or a site URL to generate keyword ideas Google Sets for automatically creating sets of items from a few examples Open Calais is free limited API web service to automatically attach semantic metadata to content, based on either entities people, places, organizations, etc.
The metadata results are stored centrally and returned to you as industry-standard RDF constructs accompanied by a Globally Unique Identifier GUID Query-by-document from BlogScope has a nice phrase extraction service, with a choice of ranking methods. Can also be used in a Firefox plug-in not texted with 3. The tags are chosen based on both statistical and linguistic analysis of the original text Tagthe. Tags can be single words only. The tool also recognizes named entities such as people names and locations TermExtractor extracts terminology consensually referred in a specific application domain.
TermFinder uses Poisson statistics, the Maximum Likelihood Estimation and Inverse Document Frequency between the frequency of words in a given document and a generic corpus of million words per language; available for English, French and Italian TerMine is an online and batch term extractor that emphasizes part of speech POS and n-gram phrase extraction.
TerMine is the terminological management system with the C-Value term extraction and AcroMine acronym recognition integrated Topia term extractor is a part-of-speech and frequency based term extraction tool implemented in python.
Here is a term extraction demo based on this tool Topicalizer is a service which automatically analyses a document specified by a URL or a plain text regarding its word, phrase and text structure.
It provides a variety of useful information on a given text including the following: Word, sentence and paragraph count, collocations, syllable structure, lexical density, keywords, readability and a short abstract on what the given text is about TrMExtractor does glossary extraction on pure text files for either English or Hungarian Wikify!
The system extracts keywords and then disambiguates and matches them to their corresponding Wikipedia definition Yahoo! Placemaker is a freely available geoparsing Web service. It helps developers make their applications location-aware by identifying places in unstructured and atomic content — feeds, web pages, news, status updates — and returning geographic metadata for geographic indexing and markup Yahoo!
The service has been reported to be shut down numerous times, but apparently is kept alive due to popular demand. COE — and its CmapTools parent — is based on the idea of concept maps. A concept map is a graph diagram that shows the relationships among concepts.
Concepts are connected with labeled arrows, with the relations manifesting in a downward-branching hierarchical structure. COE is an integrated suite of software tools for constructing, sharing and viewing OWL encoded ontologies based on these constructs Conzilla2 is a second generation concept browser and knowledge management tool with many purposes.
DL-Learner now has a flexible component based design, which allows to extend it easily with new learning algorithms, learning problems, reasoners, and supported background knowledge sources. DogmaModeler is a free and open source, ontology modeling tool based on ORM.
The philosophy of DogmaModeler is to enable non-IT experts to model ontologies with a little or no involvement of an ontology engineer; project is quite old, but the software is still available and it may provide some insight into naive ontology development Erca is a framework that eases the use of Formal and Relational Concept Analysis, a neat clustering technique. Erca is provided as an Eclipse plug-in GraphMind is a mindmap editor for Drupal.
It has the basic mindmap features and some Drupal specific enhancements. There is a quick screencast about how GraphMind looks like and what is does. It is typically used in bioinformatics drug discovery and research, toxicological studies, etc , engineering support and expert systems , and for integration of hetereogeneous data.
It supports the XTM 1. Spreadsheets can be used for initial authoring, esp if the irON guidelines are followed. It aims to connect the tradition of outline editors with emerging technologies. Its main goal is to dramatically reduce the time required to create, publish and modify vocabularies for the Semantic Web. It is written in PHP and built on the Drupal platform. These are then presented to the user, who can select terms from the list, find relations to other terms, and expand the set of terms and relations, iteratively.
Topincs is a Topic Map authoring software that allows groups to share their knowledge over the web. It makes use of a variety of modern technologies. It consists of three components: the Wiki, the Editor, and the Server.
It can export to MS Word. TemaTres is a Web application to manage controlled vocabularies, taxonomies and thesaurus. The vocabularies may be exported in Zthes, Skos, TopicMap, etc. ThManager facilitates the management of thesauri and other types of controlled vocabularies, such as taxonomies or classification schemes Vitro is a general-purpose web-based ontology and instance editor with customizable public browsing.
Vitro is a Java web application that runs in a Tomcat servlet container. The OBDM framework has garnered widespread interest in recent years, which has led to the development of advanced instruments based on this technology. These tools have been recently adopted for the development of OBDM applications for enterprise data management in various domains. One important aspect in OBDM concerns the construction of a system specification, i.
This is a complex activity, which needs various competences and adequate methodologies and tools supporting it, and this is specifically the topic addressed by the present tutorial. The tutorial leverages on the experience of the Sapienza research group on semantic technologies, which has been involved in the last years in several industrial and academic projects and has recently founded OBDA Systems, an innovative startup of Sapienza University of Rome.
After recalling the basics of OBDM, in the tutorial we will first concentrate on the ontology design task. We will translate such diagrams in Graphol, showing that these diagrams admit an essentially isomorphic representation in Graphol, which however has a precise correspondence to OWL 2. Source data analysis and mapping design will be the next topic of the tutorial. We will give an overview of the formalisms for mapping data to an ontology and will highlight the main issues arising in mapping design, as well as possible approaches to this task.
Finally, we will present tools that support the designer for the development of an OBDM specification and for the deployment of the specification over an actual source instance database. Participants will be invited to use such tools in the final hands-on-session of the tutorial. We will introduce the basic concepts related to OBDM, including the possibility of checking the ontology through intensional reasoning and performing query answering of conjunctive queries i.
We will illustrate how to build a global ontology. Then we will show how their semantics can be made precise through a translation in OWL 2. Such translation will be based on the graphical ontology language Graphol, which is in fact able to capture full OWL 2. Then we will move to data source analysis and will show how to map the data therein to elements of the ontology.
In particular we will discuss how to formulate queries over the sources and how to generate objects for the ontology through suitable constructors. We will also give some indications, coming from experience, on how to write effective mappings. The tutorial will be complemented by a hands-on session in which participants will have the possibility of trying what learned through the use of state-of-the-art OBDM tools.
In particular, to avoid the overhead of installing and configuring such tools, we plan to distribute usb pendrives with a minimal OS and all tools ready to run. Semantic enrichment to unlock the value of unstructured text and simplify the identification of new potential biomarker leads from scientific text. PoolParty Semantic Suite. Automate the handling of heterogeneous metadata systems and the creation of enterprise knowledge graphs.
Apply them to your existing taxonomies with ease. A modern annotation tool for creating training and evaluation data for machine learning models. You can also use Prodigy to help you inspect and clean your data, do error analysis and develop rule-based systems to use in combination with your statistical models.
Connect and publish complex enterprise knowledge with standard-compliant semantic graph database; Customize and apply analytics to link documents to graphs, extract new facts, classify and recommend content.
Related tools in Bio. A pre-trained weights of BioBERT, a language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc. Personalized PageRank and semantic similarity measures for linking entities found in documents to concepts from domain-specific ontologies. Imaging, Natural language processing, Data mining, Genotype and phenotype, Ontology and terminology. Prediction of human phenotype ontology term associations using cross ontology annotation co-occurrences.
Pathology, Protein interactions, Genotype and phenotype, Ontology and terminology, Gene expression. Vapur is empowered with a semantic inverted index that is created through named entity recognition and relation extraction on CORD abstracts. A Python library for materials-focused natural language processing NLP.
A web based framework that takes advantage of domain specific ontologies, and Natural Language Processing, aiming to empower exploration of biomedical resources via semantic-based querying and search.
The NLP engine analyzes the input free-text query and translates it into targeted queries with terms from the underlying ontology. It is a command-line tool to retrieve and semantically annotate results obtained from QTL mapping experiments. Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries. The process of determining correspondences between equivalent concepts in alternative ontologies, and other vocabularies.
This may include mapping to convey different levels of granularity. A service for finding mappings or cross-references between terms from ontologies, vocabularies and coding standards. Manually curated database with experimental annotations for the subcellular localizations of proteins in Homo sapiens HS, human and Arabidopsis thaliana AT, thale cress.
The process of managing ontologies and other vocabularies in semantic web-linked data environments. This includes policies for update and maintenance of constituent and new terms. Taxonomy, ontology and linked dataset management. Centree Ontology Manager. A centralised, enterprise-ready resource for ontology management and transforms the experience of maintaining and releasing ontologies for research-led businesses. A linked data server designed for ontologies. Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis.
Apache 2.
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