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Abstract

Specimen identification keys are still the most commonly created tools used by systematic biologists to access biodiversity information. Creating identification keys requires analyzing and synthesizing large amounts of information from specimens and their descriptions and is a very labor-intensive and time-consuming activity. Automating the generation of identification keys from text descriptions becomes a highly attractive text mining application in the biodiversity domain. Fine-grained semantic annotation of morphological descriptions of organisms is a necessary first step in generating keys from text. Machine-readable ontologies are needed in this process because most biological characters are only implied (i.e., not stated) in descriptions. The immediate question to ask is How well do existing ontologies support semantic annotation and automated key generation? With the intention to either select an existing ontology or develop a unified ontology based on existing ones, this paper evaluates the coverage, semantic consistency, and inter-ontology agreement of a biodiversity character ontology and three plant glossaries that may be turned into ontologies. The coverage and semantic consistency of the ontology/glossaries are checked against the authoritative domain literature, namely, Flora of North America and Flora of China. The evaluation results suggest that more work is needed to improve the coverage and interoperability of the ontology/glossaries. More concepts need to be added to the ontology/glossaries and careful work is needed to improve the semantic consistency. The method used in this paper to evaluate the ontology/glossaries can be used to propose new candidate concepts from the domain literature and suggest appropriate definitions.

Date

1. 6.2010 9:55:22

Type

a

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Abstract

In 2018, the national, bilingual authority file maintained by Library and Archives Canada (LAC), called Canadiana Authorities, underwent major changes when the internally-developed Integrated Library System (ILS) AMICUS was decommissioned and OCLC's WorldShare Management Services (WMS) was adopted as a replacement. As a part of the transition, LAC split its single, bilingual authority file Canadiana Authorities into separate English and French language files and joined Name Authority Cooperative Program (NACO) in order to manage its English-language authority records. This has been a significant change that has challenged the organization to rethink everyday practices while maintaining its commitments to the Canadian and global library community. This paper discusses this national library's history of bilingual cataloging, the reason for the changes, and the attempt to ensure that the two files "talk" to each other.

Type

a

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Abstract

Biodiversity information organization is looking beyond the traditional document-level metadata approach and has started to look into factual content in textual documents to support more intelligent and semantic-based access. This article reports the development and evaluation of CharaParser, a software application for semantic annotation of morphological descriptions. CharaParser annotates semistructured morphological descriptions in such a detailed manner that all stated morphological characters of an organ are marked up in Extensible Markup Language format. Using an unsupervised machine learning algorithm and a general purpose syntactic parser as its key annotation tools, CharaParser requires minimal additional knowledge engineering work and seems to perform well across different description collections and/or taxon groups. The system has been formally evaluated on over 1,000 sentences randomly selected from Volume 19 of Flora of North American and Part H of Treatise on Invertebrate Paleontology. CharaParser reaches and exceeds 90% in sentence-wise recall and precision, exceeding other similar systems reported in the literature. It also significantly outperforms a heuristic rule-based system we developed earlier. Early evidence that enriching the lexicon of a syntactic parser with domain terms alone may be sufficient to adapt the parser for the biodiversity domain is also observed and may have significant implications.

Type

a

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Abstract

This article presents an unsupervised algorithm for semantic annotation of morphological descriptions of whole organisms. The algorithm is able to annotate plain text descriptions with high accuracy at the clause level by exploiting the corpus itself. In other words, the algorithm does not need lexicons, syntactic parsers, training examples, or annotation templates. The evaluation on two real-life description collections in botany and paleontology shows that the algorithm has the following desirable features: (a) reduces/eliminates manual labor required to compile dictionaries and prepare source documents; (b) improves annotation coverage: the algorithm annotates what appears in documents and is not limited by predefined and often incomplete templates; (c) learns clean and reusable concepts: the algorithm learns organ names and character states that can be used to construct reusable domain lexicons, as opposed to collection-dependent patterns whose applicability is often limited to a particular collection; (d) insensitive to collection size; and (e) runs in linear time with respect to the number of clauses to be annotated.

Type

a

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Abstract

To automatically convert legacy data of taxonomic descriptions into extensible markup language (XML) format, the authors designed a machine-learning-based approach. In this project three corpora of taxonomic descriptions were selected to prove the hypothesis that domain knowledge and conventions automatically induced from some semistructured corpora (i.e., base corpora) are useful to improve the markup performance of other less-structured, quite different corpora (i.e., evaluation corpora). The "structuredness" of the three corpora was carefully measured. Basing on the structuredness measures, two of the corpora were used as the base corpora and one as the evaluation corpus. Three series of experiments were carried out with the MARTT (markuper of taxonomic treatments) system the authors developed to evaluate the effectiveness of different methods of using the n-gram semantic class association rules, the element relative position probabilities, and a combination of the two types of knowledge mined from the automatically marked-up base corpora. The experimental results showed that the induced knowledge from the base corpora was more reliable than that learned from the training examples alone, and that the n-gram semantic class association rules were effective in improving the markup performance, especially on the elements with sparse training examples. The authors also identify a number of challenges for any automatic markup system using taxonomic descriptions.

Type

a

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Abstract

Habitat information is important to biodiversity conservation and research. Extracting bacterial biotope entities from scientific publications is important to large scale study of the relationships between bacteria and their living environments. To facilitate the further development of robust habitat text mining systems for biodiversity, following the BioNLP task framework, three sequence labeling techniques, CRFs (Conditional Random Fields), MEMM (Maximum Entropy Markov Model) and SVMhmm (Support Vector Machine) and one classifier, SVMmulticlass, are compared on their performance in identifying three types of bacterial biotope entities: bacteria, habitats and geographical locations. The effectiveness of a variety of basic word formation features, syntactic features, and semantic features are exploited and compared for the three sequence labeling methods. Experiments on two publicly available BioNLP collections show that, in addition to a WordNet feature, word embedding featured clusters (although not trained with the task-specific corpus) consistently improve the performance for all methods on all entity types in both collections. Other features produce various results. Our results also show that when trained on limited corpora, Brown clusters resulted in better performance than word embedding clusters did. Further analysis suggests that the entity recognition performance can be greatly boosted through improving the accuracy of entity boundary identification.

Type

a

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Type

a