Engineering the scientific corpus: routine semantic work in (re)constructing a biological ontology

In face of the burgeoning interest in ‘ontology’ in science studies, Michael Lynch (2008) called for a move toward ‘ontography’, to talking about ontologies by way of studies in which ontologies (or at least, an ontology) are of demonstrable relevance to the doings of those being studied. This paper provides an ontography, or some part of one, in that it reports on work in ontology development being done by a group of researchers in bioinformatics, drawing its examples largely from a workshop in which some members of that group were participant and which was organised by a research network to which they belonged. Methodologies for building ‘good’ ontologies were part of the interests of this wider research group and were a motivation for the work undertaken. What is evident from our study is the fact that methods to be applied, avenues to be explored and even fundamental purposes were all in the event ‘up for grabs’ and formed a closely interlinked and mutually explicating part of the ‘logic in practice’ deployed. We will show how this research work was undertaken with reference to an existing body of knowledge, yet requiring distinctive courses of ‘discovering work’, concerning both method and substantive content. How were its results examined and reexamined in the light of ongoing, evolving and unanticipated considerations? Describing how the involved participants go about their work is, then, ‘an ontography’ in precisely the sense that Lynch proposes

Focus Issue on Legacy Information Systems and Business Process Change: Banking on the Old technology: Understanding the Organisational Context of \u27Legacy\u27 Issues

A common thread in recent discussions of organisational change is the importance of the role allocated to information technology in the realisation of such change. It is a feature of many of these discussions that IT is handled in a somewhat simplistic fashion, often with a pronounced theoretical leaning resulting in the case of the disappearing technology . Even empirical studies of new technology often fail to pay attention to the actual details of technology in use, instead focusing upon the part technology might play in producing certain managerial or workplace configurations that are themselves theoretical renderings of organisational life. By way of contrast, this paper presents some results from a long-term empirical investigation of computer systems in use in financial services that specifically aims to focus upon the actual details of technology in use. In addition it attempts to address conventional concerns with the relationship between new technology and \u27skill\u27, productivity and other factors in a rather different fashion by focusing on the issue of \u27legacy\u27. We present a number of examples of legacy issues and try to delineate their impact on everyday working life. \u27Legacy\u27, we argue, is not just a problem encountered by organisations with aging mainframes and dated software, it is an issue from the moment a computer system becomes an integral part of any organisation\u27s everyday work

Coastal fishes of the western Indian Ocean

The primary purpose of this book is to provide a means of identifying the more than 3 200 species of coastal fishes known to occur in the Western Indian Ocean (WIO). Coastal fishes are those that inhabit waters generally less than ~200 m deep, the waters over continental and insular shelves, and upper continental slopes. The book also includes some oceanic species and species that live in deeper water, but are sometimes caught in trawls in less than 200 m, or that migrate into shallower waters at night to feed. The Western Indian Ocean (WIO), as treated in these volumes, is the area between Cape Point, South Africa, and 77°34' E, at Kanyakumari (formerly Cape Cormorin), the southernmost point of India, and to 40° S, just south of St Paul Island. Although considered as separate water bodies, the Red Sea and Persian/Arabian Gulf have been included. Some contributors have also chosen to include species from Sri Lanka. The region thus encompasses the entire east and southern coasts of Africa, Madagascar and the various island clusters of the Comoros, the Seychelles, the Maldive and Lakshadweep islands, the Chagos Archipelago and the islands and sea mounts of the Mascarene Plateau, to as far as 40° S, and thus some fishes from St Paul and Amsterdam Islands have been included. This large expanse, stretching from tropical waters of the northwestern Indian Ocean to the warm temperate waters of False Bay, South Africa, includes a number of poorly known biogeographic areas. A map of the entire Indian Ocean is placed on the inside front cover of each printed volume, with some areas in greater detail on the inside back cover. The book does not include distribution maps for species, but gives localities from which species are known, with emphasis on WIO localities; our understanding of distributions of many species is often incomplete. Fishes are the most abundant and diverse group of vertebrates and have colonised every aquatic habitat on Earth: the oceans, lakes, rivers and caves, from polar seas at –2 °C to hot, freshwater springs at 44 °C, and from tropical reefs and mangrove forests to the deepest ocean depths. Fishes are also the most poorly known group of vertebrates. In the 2006 edition of Joseph Nelson’s Fishes of the World the estimate of the number of species of extant fishes worldwide stood at about 23 000. This number is growing annually, and was thought to be about 33 460 species at the end of 2016 (www.fishwisepro.com). Between the years 2000 and 2015 an average of 150 new species of marine fishes were described each year – of which 10% of the total (156 species) were from the WIO. The WIO is home to about 15% of all the marine fish species in the world’s oceans. Another measure of the diversity of fishes of this area is its relatively high level of endemicity, particularly around southern Africa and in the Red Sea. About 13% of southern African marine fishes are endemic, most of these in only five families: Clinidae with about 44 endemic species, Gobiidae with 28, Sparidae with 28, Pentanchidae with 6, and Batrachoididae with 7 endemic species. In the Red Sea at least 170 of the more than 1100 species are endemic. The WIO region is also home to a large human population, representing a wide range of ethnic and cultural backgrounds. The area includes the countries of South Africa, Mozambique, Tanzania, Kenya, Somalia, Eritrea, Sudan, Egypt, Israel, Jordan, Saudi Arabia, Yemen, Oman, United Arab Emirates, Qatar, Bahrain, Kuwait, Iraq, Iran, Pakistan, India and Sri Lanka, as well as the many island nations and territories. Many of the people living in coastal areas are dependent on fish catches and other marine resources for both sustenance and often a livelihood, as highly diversified artisanal fisheries make up the bulk of the fishing effort in the region. And, as elsewhere in the world, many of the fish resources have been compromised by commercial interests (including those of other countries), often leaving fish stocks in a poor state. This book has a number of purposes, all of which coalesce around providing users with a better understanding of the area’s fishes and their environment. Accordingly, it includes a number of background chapters covering subjects as diverse as the oceanography of the region, and the history and evolution of the bony fishes. In recent years genetic analysis has proved to be a powerful tool for taxonomists. In many instances molecular results have caused taxonomists to rethink both the definitions of certain taxa and the interrelationships of taxa. In some instances, what were long considered cohesive (monophyletic) taxa were found to include groups of fishes that are in fact not closely related (paraphyletic), while in other instances taxa thought to be distinct were found not to be, meriting their merging with other existing taxa. At times, long-accepted family groups have been divided into two or more distinct families, or separate families have been combined into a single one. Where possible such changes in our understanding of the relationships of fishes are reflected in these volumes. Where some contributors have taken a more conservative approach by awaiting more research and not adopting these changes, alternative taxonomies are noted (see also the introductory chapter on Naming organisms and determining their relationships). For each species in the book, the literature pertinent to that species in the WIO is given: the original species description reference, synonyms for the region and other important taxonomic and biological references. For many commercially important species or fishes of interest to anglers there is additional information on life history, size and capture, and for some but not all species, their IUCN conservation status if Near Threatened, Vulnerable, Endangered or Critically Endangered (in the first instance, valid at the time of writing. See www.iucnredlist.org for current information. Note: we have not included the IUCN conservation status where species are of Least Concern or Data Deficient). Most species are illustrated with photographs, drawings or paintings. Colour photographs and paintings are provided on plates for each volume.1st Editio

Explicating the challenges of providing novel media experiences driven by user personal data

The turn towards personal data to drive novel media experiences has resulted in a shift in the priorities and challenges associated with media creation and dissemination. This paper takes up the challenge of explicating this novel and dynamic scenario through an interview study of employees delivering diverse personal data driven media services within a large U.K. based media organisation. The results identify a need for better interactions in the user-data-service ecosystem where trust and value are prioritised and balanced. Being legally compliant and going beyond just the mandatory to further ensure social accountability and ethical responsibility as an organisation are unpacked as methods to achieve this balance in data centric interactions. The work also presents how technology is seen and used as a solution for overcoming challenges and realising priorities to provide value while preserving trust within the personal data ecosystem

The Allen Telescope Array: The First Widefield, Panchromatic, Snapshot Radio Camera for Radio Astronomy and SETI

The first 42 elements of the Allen Telescope Array (ATA-42) are beginning to deliver data at the Hat Creek Radio Observatory in Northern California. Scientists and engineers are actively exploiting all of the flexibility designed into this innovative instrument for simultaneously conducting surveys of the astrophysical sky and conducting searches for distant technological civilizations. This paper summarizes the design elements of the ATA, the cost savings made possible by the use of COTS components, and the cost/performance trades that eventually enabled this first snapshot radio camera. The fundamental scientific program of this new telescope is varied and exciting; some of the first astronomical results will be discussed.Comment: Special Issue of Proceedings of the IEEE: "Advances in Radio Telescopes", Baars,J. Thompson,R., D'Addario, L., eds, 2009, in pres

Improved Techniques for the Surveillance of the Near Earth Space Environment with the Murchison Widefield Array

In this paper we demonstrate improved techniques to extend coherent processing intervals for passive radar processing, with the Murchison Widefield Array. Specifically, we apply a two stage linear range and Doppler migration compensation by utilising Keystone Formatting and a recent dechirping method. These methods are used to further demonstrate the potential for the surveillance of space with the Murchison Widefield Array using passive radar, by detecting objects orders of magnitude smaller than previous work. This paper also demonstrates how the linear Doppler migration methods can be extended to higher order compensation to further increase potential processing intervals.Comment: Presented at the 2019 IEEE Radar Conference in Boston earlier this yea

The Allen Telescope Array Pi GHz Sky Survey I. Survey Description and Static Catalog Results for the Bootes Field

The Pi GHz Sky Survey (PiGSS) is a key project of the Allen Telescope Array. PiGSS is a 3.1 GHz survey of radio continuum emission in the extragalactic sky with an emphasis on synoptic observations that measure the static and time-variable properties of the sky. During the 2.5-year campaign, PiGSS will twice observe ~250,000 radio sources in the 10,000 deg^2 region of the sky with b > 30 deg to an rms sensitivity of ~1 mJy. Additionally, sub-regions of the sky will be observed multiple times to characterize variability on time scales of days to years. We present here observations of a 10 deg^2 region in the Bootes constellation overlapping the NOAO Deep Wide Field Survey field. The PiGSS image was constructed from 75 daily observations distributed over a 4-month period and has an rms flux density between 200 and 250 microJy. This represents a deeper image by a factor of 4 to 8 than we will achieve over the entire 10,000 deg^2. We provide flux densities, source sizes, and spectral indices for the 425 sources detected in the image. We identify ~100$ new flat spectrum radio sources; we project that when completed PiGSS will identify 10^4 flat spectrum sources. We identify one source that is a possible transient radio source. This survey provides new limits on faint radio transients and variables with characteristic durations of months.Comment: Accepted for publication in ApJ; revision submitted with extraneous figure remove