Applications of Natural Language Processing in Biodiversity Science

Centuries of biological knowledge are contained in the massive body of scientific literature, written for human-readability but too big for any one person to consume. Large-scale mining of information from the literature is necessary if biology is to transform into a data-driven science. A computer can handle the volume but cannot make sense of the language. This paper reviews and discusses the use of natural language processing (NLP) and machine-learning algorithms to extract information from systematic literature. NLP algorithms have been used for decades, but require special development for application in the biological realm due to the special nature of the language. Many tools exist for biological information extraction (cellular processes, taxonomic names, and morphological characters), but none have been applied life wide and most still require testing and development. Progress has been made in developing algorithms for automated annotation of taxonomic text, identification of taxonomic names in text, and extraction of morphological character information from taxonomic descriptions. This manuscript will briefly discuss the key steps in applying information extraction tools to enhance biodiversity science

Ontologies as Integrative Tools for Plant Science

Premise of the study: Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the semantic web. Methods: This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: (1) comparative genetics, genomics, phenomics, and development; (2) taxonomy and systematics; (3) semantic applications; and (4) education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies.Keywords: Bio-ontologies, Plant Ontology, Plant genomics, OBO Foundry, Plant systematics, Plant anatomy, Genome annotation, Semantic web, PhenomicsKeywords: Bio-ontologies, Plant Ontology, Plant genomics, OBO Foundry, Plant systematics, Plant anatomy, Genome annotation, Semantic web, Phenomic

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

The Plant Ontology (PO;http://www.plantontology.org/" is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to > 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs.Keywords: Plant anatomy, Terpene synthase, Bioinformatics, Comparative genomics, Genome annotation, Ontolog

Simple identification tools in FishBase

Simple identification tools for fish species were included in the FishBase information system from its inception. Early tools made use of the relational model and characters like fin ray meristics. Soon pictures and drawings were added as a further help, similar to a field guide. Later came the computerization of existing dichotomous keys, again in combination with pictures and other information, and the ability to restrict possible species by country, area, or taxonomic group. Today, www.FishBase.org offers four different ways to identify species. This paper describes these tools with their advantages and disadvantages, and suggests various options for further development. It explores the possibility of a holistic and integrated computeraided strategy

Weed Women, All Night Vigils, and the Secret Life of Plants: Negotiated Epistemologies of Ethnogynecological Plant Knowledge in American History

This dissertation critiques the discourse of traditional ecological knowledge described as embedded in indigenous peoples\u27 longevity in location, for the purpose of understanding the embodiment of ecological knowledge in culture. The aim of this research is to examine the historical and epistemic complexity of traditional ecological knowledge that may be both established from the length of time people reside in a specific ecosystem and constitutive of negotiations between and among different cultures. I choose the specific case of the negotiation of plant knowledge for women\u27s reproductive health among Native, African, and European groups as those negotiations unfolded on the American continent from European settlement in the early 17th century to the post-Emancipation period of the early 20th century. By focusing on ethnobotanical accounts of women\u27s reproductive health knowledge I explain how this knowledge persisted or changed as people moved, and how this knowledge might have been created through negotiations across cultural boundaries. It is my contention that traditional ecological knowledge is simultaneously maintained and altered through peoples migrations and negotiations. To test this contention I ask a number of key questions from my analysis of historical ethnogynecological evidence. To what extent is traditional ecological knowledge embodied in people and to what extent is it emplaced in an ecosystem? How is the traditional ecological knowledge of longevity in place different from traditional ecological knowledge that shifts as people migrate? What is the evidence that traditional ecological knowledge is formed through negotiations across boundaries of culture, race, and epistemology, and does this change the framing of traditional ecological knowledge discourse? My research conceives of a discourse of traditional ecological knowledge that explicitly addresses issues of both ecologically emplaced knowledge and culturally embedded knowledge. I demonstrate that an understanding of traditional ecological knowledge formulated on the way knowledge moves and is shared provides a fuller and more dynamic discourse of traditional ecological knowledge

CHARACTERIZING DROUGHT ADAPTATIONS, PHENOTYPIC PLASTICITY, AND FIXED GENE EXPRESSION PATTERNS WITHIN QUERCUS

This dissertation was written on topics related to the genus Quercus with a primary focus on Quercus ellipsoidalis (northern pin oak) and Quercus rubra (northern red oak). Within this dissertation are chapters related to the setup of experimental common gardens within the Ford and Kellogg experimental forest, a literature review describing drought adaptations of Quercus sect. Lobatae (red oak group), identification of transcription factors within the Q. robur (English oak) and Q. rubra genomes, a study comparing leaf trait phenotypic plasticity of Q. ellipsoidalis and Q. rubra, and an RNA-seq experiment studying ecological speciation between Q. ellipsoidalis and Q. rubra. Within these studies, I found that Q. ellipsoidalis and Q. rubra have similar leaf trait phenotypic plasticity, and unique molecular phenotypes related to upregulation of genes related to photosynthesis and innate immune response, respectively. Within the Q. rubra genome, I identified multiple regions of transcription factor gene clusters that could have a significant role related to drought adaptation for this species

Growing Intercommunalist "pockets of resistance" with Aloha 'Aina in Hawai'i

In der hawaiianischen Vorstellung steht das Land in einer Kinship- oder Verwandtschaftsbeziehung als lebendes und atmendes Familienmitglied, von dem man abstammt. Aloha 'Aina („Liebe zum Land“) ist eine Onto-Epistemologie der Indigenen auf Hawai'i, analog zu anderen gemeinschaftlichen Organisationsformen, die Mensch, Nicht-Mensch und Natur als miteinander verbunden betrachten, wie etwa im Glauben der Haudenosaunee. Anstatt Aloha 'Aina als eine Methode der „dekolonialen Klimagerechtigkeit“ zu präsentieren, die im globalen Norden nachgeahmt werden soll, und damit Aloha 'Aina von jenem „Land“ zu entfernen, theoretisiere ich ein ortsbezogenes Konstrukt, das ich „Spirit of Relationality“ nenne. Ich verknüpfe das hawaiianische Aloha 'Aina mit der politischen Theorie des Interkommunalismus des Black Panther Huey P. Newton, um dekoloniale Formen globaler Klimagerechtigkeit für nicht-Indigene Positionalitäten zu entwickeln. Der Zweck dieser Verbindung war es, den „Geist“ innerhalb der postmarxistischen Theorien neu zu verorten, wie sie von Vanessa Watts (Haudenosaunee & Anishinaabe) kritisiert werden, da dieser Geist für eurozentrische Perspektiven entfernt wurde. Indem ich hawaiianische Geschichten und zeitgenössische Poesie analysiere, vergleiche ich auch Vorstellungen von lokalem Glauben anderswo, wie auf den Philippinen und im Ästuargebiet, durch die Verbundenheit des Pazifiks und von fluidem Wasser und Luft. Metaphern von Spirit/Geist und Kinship, sowie eine materialistische Analyse des Antikolonialismus und der Arbeiterbewegung auf Hawaii führten dazu, dass ich meine eigenen Konzepte als „Pneumaterialismus“ bezeichnete. Dies ergibt sich aus der Metaphorik von „pneuma“ als liminaler Geist und hawaiianischem „ea“ („Atem,“ „Leben,“ „Wiederaufleben“), mit Wortspielen zur Metaphysik und Antagonismen zwischen Materialismus/Materie und Idealismus. Die Dynamik interkultureller und organischer Symbiosen und indigener Solidaritäten bildet ebenfalls die Grundlage dieser Metaphern.In Indigenous Hawaiian conceptualization land is relational, a living and breathing family member that one is descended from. Aloha 'Aina (“love of the land”) is an Indigenous way of knowing and being in Hawai'i, analogous to other communal forms of organization that consider human, non-human, and nature as interrelated, such as in Haudenosaunee beliefs. Instead of presenting Aloha 'Aina as a method of “decolonial climate justice” to emulate within the global North, and thus remove Aloha 'Aina from its land, I theorize a place-based construct I call “spirit of relationality.” I connect Hawaiian Aloha 'Aina with Black Panther Huey P. Newton’s political theory of Intercommunalism towards decolonial forms of global climate justice for non-Indigenous positionalities. The purpose of this connection was to relocate “spirit” within post-Marxist theories, as critiqued by Vanessa Watts (Haudenosaunee & Anishinaabe) of having been removed for Eurocentric perspectives. Analyzing Hawaiian stories and contemporary poetry, I also compare notions of localized beliefs elsewhere, such as in the Philippines and in the estuary space, through the connectedness of the Pacific Ocean, in-flux waters, and air. Metaphors of spirit/ghost and kinship, as well as materialist analysis of anticolonialism and labor organizing in Hawai'i, led to labelling my own concepts as “Pneumaterialism.” This is from metaphors of “pneuma” as in-between spirit and Hawaiian “ea” (“breath,” “life,” “resurgence”), with wordplay on metaphysics and antagonisms between materialism/matter and idealism. Dynamics of intercultural and organic symbiosis and Indigenous solidarities also ground these metaphors

Forest insects, personhood and the environment: Harurwa (edible stinkbugs) and conservation in south-eastern Zimbabwe

Includes bibliographical references.This study critically examines the possibilities for the mutual, symbiotic coexistence of human beings, biological organisms (a unique species of insects), and natural forests in a specific environment, Norumedzo, in the south-eastern region of rural Zimbabwe. Based on ethnographic fieldwork undertaken in the aforementioned region between December 2011 and December 2012, the study interrogates the enlightenment modernist paradigmatic oppositions such as science versus indigenous knowledge and nature versus culture and as such forms part of a major epistemological shift in Anthropology towards rethinking the binaries created by enlightenment modern thought which have for so long served to confine anthropological attention to the social. The study advances the argument that modernist divides/binaries are artificial and impede understanding of environmentalities, especially of relationships between social ‘actors’ in any given space, given that mutual relationships and interactions between humans and other beings as well as between diverse epistemologies are an effective proxy of nurturing ‘sustainable’ conservation. The study demonstrates how some aspects of the emerging body of literature in the post-humanities and relational ontologies can work to grasp the collaborative interactional space for different social “actors” in the environment through which knowledge communities can be extended. Given that the post-humanities approach advanced in this work focuses attention on relationships among people, animals, ancestors, and things, it rethinks the enlightenment modernist division of the world into subjects and objects, that is, into humans and things. Rethinking those divisions enables fresh conversations between the [Western] sciences and other knowledge forms especially indigenous epistemologies. In this study, the rethinking of those divides is facilitated by an anthropological exploration of the social interconnectedness and mutual interdependence of rural Zimbabweans, forest insects known as edible stinkbugs (harurwa in vernacular) and the natural forests which, in fact, are critical to understanding the eco-systemic knowledges upon which livelihoods of many rural Zimbabweans are hinged

Tools for identifying biodiversity: progress and problems

The correct identification of organisms is fundamental not only for the assessment and the conservation of biodiversity, but also in agriculture, forestry, the food and pharmaceutical industries, forensic biology, and in the broad field of formal and informal education at all levels. In this book, the reader will find short presentations of current and upcoming projects (EDIT, KeyToNature, STERNA, Species 2000, Fishbase, BHL, ViBRANT, etc.), plus a large panel of short articles on software, taxonomic applications, use of e-keys in the educational field, and practical applications. Single-access keys are now available on most recent electronic devices; the collaborative and semantic web opens new ways to develop and to share applications; the automatic processing of molecular data and images is now based on validated systems; identification tools appear as an efficient support for environmental education and training; the monitoring of invasive and protected species and the study of climate change require intensive identifications of specimens, which opens new markets for identification research