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Peer-To-Peer Databases for e-Science: a Biodiversity Case Study

Daniela Alvarez, Ale Smukler, Alejandro A. Vaisman
2005 Brazilian Symposium on Databases  
Based on this idea, we present an implementation (along with preliminary testing results), introduce a data model and a query language for biodiversity databases, and show that our proposal can be easily  ...  A join through the TSN -Taxonomic Serial Number of the species -is performed. Queries over different domain implementations are performed in an independent fashion.  ...  SELECT taxonomic units.unit name1¡ , taxonomic units.unit name2¡ DOMAIN biologicaltaxonomicdata¡ COMPONENTS taxonomic units¡ ¢ jurisdiction¡ WHERE taxonomic units.tsn¡ = jurisdiction.tsn¡ AND jurisdiction.jurisdiction  ... 
dblp:conf/sbbd/AlvarezSV05 fatcat:bke5bwcegfg7jhu4m745doc3dy

Semedico: A Comprehensive Semantic Search Engine for the Life Sciences

Erik Faessler, Udo Hahn
2017 Proceedings of ACL 2017, System Demonstrations  
SEMEDICO is a semantic search engine designed to support literature search in the life sciences by integrating the semantics of the domain at all stages of the search process-from query formulation via  ...  query processing up to the presentation of results.  ...  This way, SEMEDICO prefers query matches on shorter text passages over those in larger ones.  ... 
doi:10.18653/v1/p17-4016 dblp:conf/acl/FaesslerH17 fatcat:folqg7czdbdsdo5z6uqfnw2e5a

TaxoPublish: Towards a solution to automatically personalize taxonomies in e-catalogs

Heiko Angermann, Naeem Ramzan
2016 Expert systems with applications  
The existing works need an explicit user-query, are missing information about the domain, or require the modification through the provider.  ...  domains.  ...  This highlights that Past-Term TaxoPublish already performs with very high correctness over different e-commerce domains.  ... 
doi:10.1016/j.eswa.2016.08.058 fatcat:ikjhfkaeancmdd3ou3bkwxjco4

Constructing a biodiversity terminological inventory

Nhung T. H. Nguyen, Axel J. Soto, Georgios Kontonatsios, Riza Batista-Navarro, Sophia Ananiadou, Robert Guralnick
2017 PLoS ONE  
An assessment of the interface by domain experts reveals that our query expansion based on related names is useful for increasing the number of relevant documents retrieved.  ...  Domain-specific terminological resources, which include term variants, synonyms and related terms, are thus important in supporting semantic search over large textual archives.  ...  Whilst three of the queries were pre-supplied by us, for the other three, the users were asked to enter their own preferred species names belonging to any of the following three taxonomic classes: "Aves  ... 
doi:10.1371/journal.pone.0175277 pmid:28414821 pmcid:PMC5393592 fatcat:dmpe4wsw75fdlj4nvprnchqski

Materializing multi-relational databases from the web using taxonomic queries

Matthew Michelson, Sofus A. Macskassy, Steven N. Minton, Lise Getoor
2011 Proceedings of the fourth ACM international conference on Web search and data mining - WSDM '11  
Creating seeds often requires more domain knowledge than taxonomic queries, and previous work has shown that extraction methods may be sensitive to which input seeds they are given.  ...  Further, our approach uses taxonomic queries to bootstrap the extraction, rather than the more traditional "seed instances."  ...  We use the domain name rather than the specific taxonomic query for the column, since relevant columns can be related to a domain without being specifically related to the taxonomic query.  ... 
doi:10.1145/1935826.1935885 dblp:conf/wsdm/MichelsonMMG11 fatcat:dnbhewbuovdfvbaupxafez75dq

Learning non-taxonomic relationships from web documents for domain ontology construction

David Sánchez, Antonio Moreno
2008 Data & Knowledge Engineering  
The discovery of non-taxonomic relationships is often neglected, even though it is a fundamental point in structuring domain knowledge.  ...  It is able to discover domain-related verbs, extract non-taxonomically related concepts and label relationships, using the Web as corpus.  ...  are rejected (is/are, include, etc.) as it is preferred to treat the taxonomic case is treated independently.  ... 
doi:10.1016/j.datak.2007.10.001 fatcat:lhkdrvccfvg37hjty2z25omsmu

Berkeley PHOG: PhyloFacts orthology group prediction web server

Ruchira S. Datta, Christopher Meacham, Bushra Samad, Christoph Neyer, Kimmen Sjölander
2009 Nucleic Acids Research  
PHOG is based on pre-computed trees in the PhyloFacts resource, and contains over 366 K orthology groups with a minimum of three species.  ...  the TreeFam-A manually curated orthology database show that PHOG provides a combination of high recall and precision competitive with both InParanoid and OrthoMCL, and allows users to target different taxonomic  ...  The second table displays a table of all orthologs found over all PHOGs containing the query, listed in alphabetic order by taxonomic origin.  ... 
doi:10.1093/nar/gkp373 pmid:19435885 pmcid:PMC2703887 fatcat:3y57ur55lvh3ffulsy3xnm4rei

Taxonomy-based relaxation of query answering in relational databases

Davide Martinenghi, Riccardo Torlone
2014 The VLDB journal  
Traditional information search in which queries are posed against a known and rigid schema over a structured database is shifting toward a Web scenario in which exposed schemas are vague or absent and  ...  We first propose a conservative extension of the relational algebra for this model in which special operators allow the specification of relaxed queries over vaguely structured information.  ...  based on resource similarity [9] , and by exploiting domain knowledge and user preferences [20] .  ... 
doi:10.1007/s00778-013-0350-x fatcat:4r3fhmye6zgjdg77r7gknqaqfi

Natural Selection: Finding Specimens in a Natural History Collection [chapter]

Marieke van, Antal van den Bosch, Steve Hunt, Marian van der Meij, Rene Dekker, Piroska Lendvai
2011 Changing Diversity in Changing Environment  
The domain knowledge comes from taxonomic and geographic resources (see Subsections 4 and 4), a domain ontology, domain-specific rules and analysis of typical queries in the domain.  ...  On its own, the COMPLEX query mode improves the mean average precision with 5.83% over the ALL query mode, and with 7.59% for the ANY query mode.  ... 
doi:10.5772/25206 fatcat:6bfejpb3pzarfi2we6uyqrvg4m

An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP)

Dongying Wu, Amber Hartman, Naomi Ward, Jonathan A. Eisen, Jean-Nicolas Volff
2008 PLoS ONE  
It generates both high-quality multiple sequence alignments and phylogenetic trees, and thus can be used for multiple purposes including phylogenetically-based taxonomic assignments and analysis of species  ...  Step 2 makes an initial approximate taxonomic identification of the query sequence within that domain. Step 3 does a fine-scale phylogenetic analysis within the taxonomic group identified in Step 2.  ...  The three-domain subset. A separate three-domain subset including sequences from all three domains of life was prepared solely for use in assigning query sequences to a domain.  ... 
doi:10.1371/journal.pone.0002566 pmid:18596968 pmcid:PMC2432038 fatcat:s3csvl2dozghlp7oafigvy7iui

Personalized information retrieval based on context and ontological knowledge

2008 Knowledge engineering review (Print)  
Context modeling has long been acknowledged as a key aspect in a wide variety of problem domains.  ...  Based on a formal grounding at the representational level, we propose methods for the automatic extraction of persistent semantic user preferences, and live, ad-hoc user interests, which are combined in  ...  over time following the previous methodology and her related queries, that is, Elli's profile is now enhanced and includes the weighted semantic interests for domain concepts of the ontology shown next  ... 
doi:10.1017/s0269888907001282 fatcat:rofjdobmufeuhfcqgvym7vgvcu

STC: Semantic Taxonomical Clustering for Service Category Learning [article]

Sourish Dasgupta, Satish Bhat, Yugyung Lee
2013 arXiv   pre-print
In this paper, we have proposed a self-organizing based clustering algorithm called Semantic Taxonomical Clustering (STC) for taxonomically organizing services with self-organizing information and knowledge  ...  This is because of higher universal preference of the Plug-in match over the Subsume match that assumes the match strength order is preserved for both the Input and the Output features.  ...  queries ( ) that have been mapped over the cluster We first observed the performance of STC over the O-cluster space with respect to each of the 29 OWLS-TC queries (O-cluster space query accuracy).  ... 
arXiv:1303.5926v1 fatcat:pza5y7lzgvhlxnc273fyrn4q6i

A Contextual Personalization Approach Based on Ontological Knowledge

David Vallet, Miriam Fernández, Pablo Castells, Phivos Mylonas, Yannis Avrithis
2006 European Conference on Artificial Intelligence  
Towards that scope, we propose a novel contextual knowledge modeling scheme, and an approach for the dynamic, contextual activation of semantic user preferences to better represent user interests in coherence  ...  of preferences over time.  ...  Given the domain ontology O, we define the set of all preferences over O as PO = [0, 1] |O| , where given p ∈ PO, the value px represents the preference intensity for a concept x ∈ O in the ontology.  ... 
dblp:conf/ecai/ValletFCMA06 fatcat:oi6no7hhnjhbhgwo3qnz5o6p7q

Personalisation Services for Self E-learning Networks [chapter]

Kevin Keenoy, Alexandra Poulovassilis, Vassilis Christophides, Philippe Rigaux, George Papamarkos, Aimilia Magkanaraki, Miltos Stratakis, Nicolas Spyratos, Peter Wood
2004 Lecture Notes in Computer Science  
The proposed personalisation facilities include: querying learning object descriptions to return results tailored towards users' individual goals and preferences; the ability to define views over the learning  ...  Declarative Queries and Views Finding LOs in a SeLeNe will rely on RQL, a declarative query language offering browsing and querying facilities over RDF/S descriptions.  ...  The SeLeNe will also provide browsing and searching facilities over the LO information space, which return results tailored towards users' individual goals and preferences.  ... 
doi:10.1007/978-3-540-27834-4_27 fatcat:3sy4nopbnve43dwoym7x5tm63y

How users interact with biodiversity information using TaxonTree

Bongshin Lee, Cynthia Sims Parr, Dana Campbell, Benjamin B. Bederson
2004 Proceedings of the working conference on Advanced visual interfaces - AVI '04  
Users with different levels of interest in the domain had different interaction preferences.  ...  Many other domains share this problem. We developed an interface, TaxonTree, to visualize the taxonomic hierarchy of animal names.  ...  Most users preferred browsing the tree over searching.  ... 
doi:10.1145/989863.989918 dblp:conf/avi/LeePCB04 fatcat:z44x5fqt5jhw3ata5psvrws2fi
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