Open Biomedical Ontologies

Top PDF Open Biomedical Ontologies:

Ontology-Based Querying with Bio2RDF’s Linked Open Data

Ontology-Based Querying with Bio2RDF’s Linked Open Data

Of the 19 datasets, InterPro, BioPortal and iRefIndex are collections of multiple indi- vidual datasets. InterPro contains 12 datasets: CATH, Gene3D, PANTHER, PIRSF, Pfam, PRINTS, ProDom, PROSITE, HAMAP, SMART, SUPERFAMILY and TIGR- FAMs. iRefIndex consists of 13 datasets (BIND, BioGRID, CORUM, DIP, HPRD, Inna- teDB, IntAct, MatrixDB, MINT, MPact, MPIDB, MPPI and OPHID). The Bio2RDF version of BioPortal currently only consists of 107 Open Biomedical Ontologies (OBO) ontologies including ChEBI, Protein Ontology and the Gene Ontology, and efforts are being made to coordinate with the NCBO BioPortal team to make use of their emer- ging SPARQL endpoint.Each dataset in the Bio2RDF network is connected to all the other datasets, either directly through a named reference or indirectly through some path through the data. Figure 1A shows how the new and updated Bio2RDF datasets are interconnected while Figure 1B shows detailed connectivity for the Pharmacoge- nomics Knowledge Base (PharmGKB). PharmGKB links to the following datasets (with their corresponding namespace): Allele Frequency Database (alfred), BindingDB (bin- dingdb), Chemical Entities of Biological Interest (chebi), Comparative Toxicogenomics Database (ctd), NLM ’ s DailyMed (dailymed), Health Canada Drug Product Database (dpd), DrugBank (drugbank), Ensembl (ensembl), GenAtlas (genatlas), NCBI Gene (geneid), PDB Heteroatom Vocabulary (het), Database of Human Unidentified Gene- Encoded Large Proteins Analyzed (huge), Human CYC (humancyc), International Union of Pharmacology Ligands (iupharligand), Kyoto Encyclopedia of Genes and Gen- omes (kegg), Medical Subject Headings (mesh), ModBase Database of Comparative Protein Structure Models (modbase), National Drug Code Directory (ndc), Online Mendelian Inheritance in Man (omim), PubChem (pubchem), Refseq (refseq), Systema- tized Nomenclature of Medicine (snomed), HGNC Gene Symbols (symbol),Therapeutic
Show more

13 Read more

SNOMED CT standard ontology based on the ontology for general medical science

SNOMED CT standard ontology based on the ontology for general medical science

The ontological foundations of the large clinical ter- minology in SCT have substantially evolved; the Inter- national Health Terminology Standards Development Organization (IHTSDO) [3] and Gao and Khazai [30] showed how SCT conforms to the OWL standards. However, there are no upper-level ontologies to de- scribe the SCT concept model (SCM) [31], i.e. formal or semiformal systems of categories, relationships, and axioms. Héja et al. [32] and Lopez-Garcia and Schulz [33] asserted that the SCT ontology (SCTO) is error prone without alignment with highly constrained and formal upper-level ontologies, such as BFO, Descriptive Ontology for Linguistic and Cognitive Engineering (DOLCE), or BioTopLite [1, 31, 34]. Rodrigues et al. [35] asserted that to build a common ontology, you have to agree on a common model of meaning. Although SCT is published twice a year (January and July) in Release Format 2 (RF2), the 19 top-level con- cepts are not changed between these releases; new re- leases mainly try to fix redundancies, inconsistencies, errors, and shortages [6, 36]. For each new release, IHTSDO provides textual release notes and delta files to determine the atomic additions and removals of con- cepts and relationships [7]. However, SCT top-level concepts or categories, which are formally modeled by the SCM, are stable. The Open Biomedical Ontologies (OBO) Foundry advocates the use of an upper-level ontology [37]. Using a common upper-level ontology for building the SCTO has several advantages, such as
Show more

19 Read more

Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens

Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens

IMPC: International Mouse Phenotyping Consortium; MP: Mammalian phenotype; MGI: Mouse genome informatics; OWL: Ontology web language; OBO: Open biomedical ontologies; RGD: Rat genome dat[r]

7 Read more

RKB: a Semantic Web knowledge base for RNA

RKB: a Semantic Web knowledge base for RNA

Here, we describe an RNA knowledge base (RKB) for structure-oriented knowledge using RDF/OWL Semantic Web technologies. RKB extends the RNAO, an RNA ontol- ogy jointly developed with the RNA Ontology Consortium [5], and builds on other Open Biomedical Ontologies (OBO) for information content entities (e.g. PDB files, structure models), real world entities (e.g. base pairs, base stacks) and their qualities (e. g. nucleoside/sugar conformations). RKB is populated from RNA-specific PDB entries and base pairing/stacking identified by MC-Annotate. We demonstrate how the result- ing knowledge base supports powerful question answering over OWL-DL ontologies using a description logic system.
Show more

10 Read more

An Overview of the CRAFT Concept Annotation Guidelines

An Overview of the CRAFT Concept Annotation Guidelines

annotation, we are employing the full sets of terms, ranging from approximately one thousand to several tens of thousands of terms, of select ontologies of the Open Biomedical Ontologies (OBO) Consortium, the most prominent set of biomedical ontologies (Smith et al., 2007), as well as several other significant large biomedical controlled terminologies. The terms of these on- tologies and terminologies, which serve as the classes of the semantic annotation schema for the this corpus, are continually under development by biomedical researchers and knowledge engi- neers and are widely used throughout the bio- medical field, as opposed to other annotation schemas that are often idiosyncratic and not like- ly reusable for other tasks. Furthermore, though these ontologies have been used for a variety of NLP tasks, they have not been used in their en- tirety toward gold-standard markup of text.
Show more

5 Read more

Biomedical Semantics: the Hub for Biomedical Research 2.0

Biomedical Semantics: the Hub for Biomedical Research 2.0

JBMS aims at publishing interdisciplinary research that crosses the traditional bound- aries between the involved disciplines (i.e. biology, medicine, mathematics, computer science, bioinformatics) and areas (knowledge representation, information retrieval, data mining, reasoning and visualisation). The journal will therefore aim to attract contribu- tions that are currently scattered over journals in different fields, and are typically focused on the perspective of a particular discipline (where the publication will be deposited), rarely addressing the entire complexity of biomedical semantic modelling and usage. The full scope of topics of interest is given on the journal's About page. The two main topic areas of the journal are:
Show more

5 Read more

Results of the ontology alignment evaluation initiative 2018

Results of the ontology alignment evaluation initiative 2018

The track uses several reference alignments for evaluation: the old (and not fully complete) manually curated open reference alignment, ra1; an extended, also manu- ally curated version of this alignment, ra2; a version of the latter corrected to resolve violations of conservativity, rar2; and an uncertain version of ra1 produced through crowd-sourcing, where the score of each correspondences is the fraction of people in the evaluation group that agree with the correspondence. The latter reference was used in two evaluation modalities: discrete and continuous evaluation. In the former, corre- spondences in the uncertain reference alignment with a score of at least 0.5 are treated as correct whereas those with lower score are treated as incorrect, and standard evalu- ation parameters are used to evaluated systems. In the latter, weighted precision, recall and F-measure values are computed by taking into consideration the actual scores of the uncertain reference, as well as the scores generated by the matching system. For the sharp reference alignments (ra1, ra2 and rar2), the evaluation is based on the stan- dard parameters, as well the F 0.5 -measure and F 2 -measure and on conservativity and
Show more

42 Read more

Embedding Biomedical Ontologies by Jointly Encoding Network Structure and Textual Node Descriptors

Embedding Biomedical Ontologies by Jointly Encoding Network Structure and Textual Node Descriptors

GRAM model (Mikolov et al., 2013) is then used to learn node embeddings that successfully pre- dict the nodes in each walk, from the node at the beginning of the walk. To enrich the node em- beddings with information from their textual de- scriptors, we replace the NODE 2 VEC look-up ta- ble with various architectures that operate on the word embeddings of the descriptors. These in- clude simply averaging the word embeddings of a descriptor, and applying recurrent deep learning encoders. The proposed method can be seen as an extension of NODE 2 VEC that incorporates textual node descriptors. We evaluate several variants of the proposed method on link prediction, a stan- dard evaluation task for NE methods. We use two biomedical networks extracted from UMLS (Bo-
Show more

11 Read more

Biomedical Research| Open Access Journals

Biomedical Research| Open Access Journals

actinomycetemcomitans invasion induced secretion of interleukin (IL)-1 β and expression of inflammasome-associated factors, including nucleotide-binding oligomerization domai[r]

8 Read more

Biomedical Research| Open Access Journals

Biomedical Research| Open Access Journals

Alteration of haematological parameters can combine with other clinical and laboratory markers which will help physician to early diagnosis of dengue fever in the first day of admi[r]

5 Read more

Biomedical Research| Open Access Journals

Biomedical Research| Open Access Journals

For the mechanical testing, four-point bending fixture was used for the static bending test and fatigue test but the torsion test, there was a different fixture were used so the multi[r]

6 Read more

Enrichment of French Biomedical Ontologies with UMLS Concepts and Semantic Types for Biomedical Named Entity Recognition Though Ontological Semantic Annotation

Enrichment of French Biomedical Ontologies with UMLS Concepts and Semantic Types for Biomedical Named Entity Recognition Though Ontological Semantic Annotation

In the context of the Semantic Indexing of French Biomedical Data Resources (SIFR) project, we have developed the SIFR BioPortal (http://BioPortal.lirmm.fr) Jonquet et al. (2016), an open platform to host French biomedical ontologies and terminologies based on the technology developed by the US National Center for Biomedical Ontology (Noy et al., 2009; Whetzel and Team, 2013). The portal facilitates the use and fostering of ontologies by offering a set of services such as search and browsing, mapping hosting and generation, metadata edition, versioning, visualization, recommendation, community feedback, etc. As of today, the portal contains 24 public ontologies and terminologies (+ 6 private ones) that cover multiple areas of biomedicine, such as the French versions of MeSH, MedDRA, ATC, ICD-10, or WHO-ART but also multilingual ontologies (for which only the French content is parsed) such as Rare Human Disease Ontology, OntoPneumo or Ontology of Nuclear Toxicity. The SIFR BioPortal includes the SIFR Annotator 2 a publicly accessible and easily usable ontology-based annotation tool to process text data in French. This service is originally based on the NCBO Annotator (Jonquet et al., 2009), a web service allowing scientists to utilize available biomedical ontologies for annotating their datasets automatically, but was significantly enhanced and customized for French. The annotator service processes raw textual descriptions input by users, tags them with relevant biomedical ontology concepts and returns the annotations to the users in several formats such as JSON-LD, RDF or BRAT. A preliminary evaluation Jonquet et al. (2016) showed that the web service matches the results of previously reported work in French, while being public, functional and turned toward semantic web standards. SIFR
Show more

8 Read more

Experiments to create ontology based disease models for
diabetic retinopathy from different biomedical resources

Experiments to create ontology based disease models for diabetic retinopathy from different biomedical resources

We propose a method to obtain ontology-based disease models consisting of a two- step process. To validate the proposal, this paper investigates to what extent we can create ontology-based disease models for DR based on BioTopLite2 and SNOMED CT using four different biomedical resources: 1) a small number of anonymised con- sultation notes; 2) the CPG for DR by the AAO [2]; 3) the BMJ Best Practice for DR [3]; and 4) the neural language models CBOW and Skip-gram of Mikolov et al. [10] produced from Deep Learning using a large corpus of scientific literature (i.e. Pub- Med [11]).
Show more

12 Read more

Using linked data for integrating educational medical web databases based on bioMedical ontologies

Using linked data for integrating educational medical web databases based on bioMedical ontologies

Open data are playing a vital role in different communities, including governments, businesses, and education. This revolution has had a high impact on the education field. Recently, Linked Data are being adopted for publishing and connecting data on the web by exposing and connecting data which were not previously linked. In the context of education, applying Linked Data to the growing amount of open data used for learning is potentially highly beneficial. This paper proposes a system that tackles the challenges of data acquisition and integration from distributed web data sources into one linked dataset. The application domain of this work is medical education, and the focus is on integrating educational content in the form of articles published in online educational libraries and Web 2.0 content that can be used for education. The process of integrating a collection of heterogeneous resources is to create links that connect the resources collected from distributed web data sources based on their semantics. The proposed system harvests metadata from distributed web sources and enriches it with concepts from biomedical ontologies, such as SNOMED CT, that enable its linking. The final result of building this system is a linked dataset of more than 10,000 resources collected from PubMed Library, YouTube channels, and Blogging platforms. The final linked dataset is evaluated by developing information retrieval methods that exploit the SNOMED CT hierarchical relations for accessing and querying the dataset. Ontology-based browsing method has been developed for exploring the dataset, and the browsing results have been clustered to evaluate its linkages. Furthermore, ontology-based query searching method has been developed and tested to enhance the discoverability of the data. The results were promising and had shown that using SNOMED CT for integrating distributed resources on the
Show more

20 Read more

Tackling Biomedical Text Summarization: OAQA at BioASQ 5B

Tackling Biomedical Text Summarization: OAQA at BioASQ 5B

We build on standard techniques such as Max- imal Marginal Relevance (Carbonell and Gold- stein, 1998) and Sentence Compression (Filip- pova et al., 2015) and incorporate domain-specific knowledge using biomedical ontologies such as the UMLS metathesaurus and SNOMEDCT (Stearns et al., 2001) to build an ideal answer gen- erator for biomedical questions. We also experi- ment with several similarity metrics such as jac- card similarity and a novel word embedding based tf-idf (w2v tf-idf) similarity metric within our sys- tem. We evaluate the performance of our system on the dataset for test batch 4 of the fourth edi- tion of the challenge and report our system per- formance on ROUGE-2 and ROUGE-SU4 (Lin and Hovy, 2003), which are the standard metrics used for official evaluation in the BioASQ chal- lenge. Our best system achieves ROUGE-2 and ROUGE-SU4 scores of 0.6534 and 0.6536 respec- tively on test batch 4 for task 4b when evaluated on BioASQ Oracle 3 . Various configurations and simi-
Show more

9 Read more

Ontology design patterns to disambiguate relations between genes and gene products in GENIA

Ontology design patterns to disambiguate relations between genes and gene products in GENIA

In biomedical IE, extracted information is frequently represented simply as untyped pairs of entities representing, for instance, protein-protein or gene-disease associations [4]. However, even resources identifying protein-protein interactions as entity pairs diverge considerably in their actual annotations [5], leading to restrictions ranging from usability to interpretability of both the annotations and IE results. In response to the limitations of such representations, there has recently been increased interest in richer representations of extracted information [6] and a number of corpora have been published that annotate associations between entities by using fine-grained types drawn from ontologies [7,8]. Yet, no definition or axiomatization of these relations has been proposed so far. Definitions and axioms are necessary to make the meaning of the relations explicit, and to provide the means for developing consistent and verifiable annotation guidelines allowing for the automatic detection of inconsistent annotations and enabling the discovery of new information through deductive inferences. Here, our aim is to define such relations and axioms for fundamental relations such as part-of connecting GGPs to referents of non-specific domain terms such as promoter region. Annotations to these fundamental relations have been introduced recently [9,10] to the widely used GENIA corpus [11].
Show more

13 Read more

Ethics of Open Access to Biomedical Research: Just a Special Case of Ethics of Open Access to Research

Ethics of Open Access to Biomedical Research: Just a Special Case of Ethics of Open Access to Research

12. Mandatory Deposit, Delayed OA. All the mandates can already require immediate deposit in all cases, speci- fying that access-privileges for any embargoed deposits may be made Closed Access rather than Open Access during the embargo [27]. This means that only their biblio- graphic metadata are accessible directly; but the Institu- tional Repositories have an email address box plus a semi- automatized "email eprint request" button that would-be users can press to request an individual copy for research purposes [31]. The author receives the email immediately and need merely click to authorize the immediate auto- matic emailing of the eprint to the requester [31]. So Green OA self-archiving mandates can already provide immediate OA for 62% of articles, and almost-immediate, almost-OA for the remaining 38%.
Show more

5 Read more

Getting to zero the biomedical way in Africa: outcomes of deliberation at the 2013 Biomedical HIV Prevention Forum in Abuja, Nigeria

Getting to zero the biomedical way in Africa: outcomes of deliberation at the 2013 Biomedical HIV Prevention Forum in Abuja, Nigeria

The implementation of biomedical HIV prevention research has engaged African stakeholders for decades. However, there has been very few opportunities and plat- forms created to enable regional stakeholders to engage with one another and discuss the required concrete con- certed actions to facilitate active ownership of the imple- mentation of HIV research on the continent. The 2013 BHPF held in Abuja, Nigeria in November 2013 made important headway in identifying the key gaps, needs, opportunities and next steps for action in the field of bio- medical HIV prevention research in Africa. The forum also created a platform that allowed for networking of sta- keholders in the field enabling them to share resources, best practices, challenges and experiences. By highlighting key considerations for biomedical HIV prevention research and development in Africa, the forum has helped identify key advocacy issues that Civil Society can expend efforts to strengthen support for future biomedical HIV prevention research in the field on the continent.
Show more

6 Read more

Ethics of Open Access to Biomedical Research: Just a Special Case of Ethics of Open Access to Research

Ethics of Open Access to Biomedical Research: Just a Special Case of Ethics of Open Access to Research

11. One of the ways the OA movement is countering the lobbying of publishers against Green OA mandates is by forming the "Alliance for Taxpayer Access." This lobbying group is focusing mainly on biomedicine, and the potential health benefits of tax-payer access to biomedical research. This is definitely a valid ethical and practical rationale for OA, but it is definitely not the sole rationale, nor the primary one.

5 Read more

Core Competencies for Scientific Editors of Biomedical Journals: Consensus Statement

Core Competencies for Scientific Editors of Biomedical Journals: Consensus Statement

high degree of congruency between the core competen- cies presented in this manuscript and editors ’ needs and ratings of importance. In fact, both the top five editor training needs and the six competency-related state- ments rated most important are all found within the 14 core competencies and/or their elements. These areas include: statistics, research methods, publication ethics, the peer review process, integrity/professionalism, good decision-making, language skills, and journal indexing. However, presented here the competencies represent a new level of collaboration and rigor in their develop- ment for scientific editors of biomedical journals. To our knowledge, these core competencies did not exist in the peer-reviewed literature previously.
Show more

10 Read more

Show all 10000 documents...