Genomic information infrastructure after the deluge

Maintaining up-to-date annotation on reference genomes is becoming more important, not less, as the ability to rapidly and cheaply resequence genomes expands

The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data

The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Initially the fields of protein–protein interactions (PPI) and mass spectroscopy have been targeted and the inaugural meeting of the PSI addressed the questions of data storage and exchange in both of these areas. The PPI group rapidly reached consensus as to the minimum requirements for a data exchange model; an XML draft is now being produced. The mass spectroscopy group have achieved major advances in the definition of a required data model and working groups are currently taking these discussions further. A further meeting is planned in January 2003 to advance both these projects

The Bacterial Soft Rot Pathogens, Pectobacterium carotovorum and P. atrosepticum, Respond to Different Classes of Virulence-Inducing Host Chemical Signals

Soft rot bacteria of the Pectobacterium and Dickeya genera are Gram-negative phytopathogens that produce and secrete plant cell wall-degrading enzymes (PCWDE), the actions of which lead to rotting and decay of their hosts in the field and in storage. Host chemical signals are among the factors that induce the bacteria into extracellular enzyme production and virulence. A class of compounds (Class I) made up of intermediate products of cell wall (pectin) degradation induce exoenzyme synthesis through KdgR, a global negative regulator of exoenzyme production. While the KdgR− mutant of P. carotovorum is no longer inducible by Class I inducers, we demonstrated that exoenzyme production is induced in this strain in the presence of extracts from hosts including celery, potato, carrot, and tomato, suggesting that host plants contain another class of compounds (Class II inducers) different from the plant cell wall-degradative products that work through KdgR. The Class II inducers are thermostable, water-soluble, diffusible, and dialysable through 1 kDa molecular weight cut off pore size membranes, and could be a target for soft rot disease management strategies

WormBase - Annotating many nematode genomes

WormBase (www.wormbase.org) has been serving the scientific community for over 11 years as the central repository for genomic and genetic information for the soil nematode Caenorhabditis elegans. The resource has evolved from its beginnings as a database housing the genomic sequence and genetic and physical maps of a single species, and now represents the breadth and diversity of nematode research, currently serving genome sequence and annotation for around 20 nematodes. In this article, we focus on WormBase’s role of genome sequence annotation, describing how we annotate and integrate data from a growing collection of nematode species and strains. We also review our approaches to sequence curation, and discuss the impact on annotation quality of large functional genomics projects such as modENCODE

The Ursinus Weekly, March 14, 1966

Dramatic arts emphasized during month of March: Ballet, theatre, motion picture • Wednesday Forum provides enjoyable evening of ballet • No exit proves cultural exchange with Beaver • Jesus, a clown? Y\u27s controversial art film asks • Senior prom to be Polynesian paradise : Cub and Key, perm. class officers, lord and lady to be named • Debating team gives excellent showing in match • Saturday\u27s movie is The list of Adrian Messinger • PSEA addressed by Miss Kelley • Curtain Club\u27s 2 one acts round out prom weekend • Political science players portray Un-American Activities Committee hearing • Editorial: Cultural exchange • Some students couldn\u27t afford Ursinus except for self-help jobs - Mr. Wentz: One-fourth of campus gets indirect aid from College; Campus ugly job: No rest or joy for bell ringer!; Waiters profess mixed feelings; Kamela fights UC litterbugs; Tour guides: Ursinus experts ; Tony unloads college linen; Proctor: Lawyer, arbiter, friend; Carolyn dodges over-cut frosh; Operator needs some training ; Librarian enjoys sadistic fun ; Blame D\u27Achille for car tickets; Guistwite gets choice of jobs! • Swim team ends season proud of 5-2 record • Intramural corner • Krum named captain at b\u27ball banquet: Troster cited as MVP • Greek gleaningshttps://digitalcommons.ursinus.edu/weekly/1220/thumbnail.jp

Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative

The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Rapid progress has been made in the development of common standards for data exchange in the fields of both mass spectrometry and protein–protein interactions since the first PSI meeting [1]. Both hardware and software manufacturers have agreed to work to ensure that a proteomics-specific extension is created for the emerging ASTM mass spectrometry standard and the data model for a proteomics experiment has advanced significantly. The Protein–Protein Interactions (PPI) group expects to publish the Level 1 PSI data exchange format for protein–protein interactions by early summer this year, and discussion as to the additional content of Level 2 has been initiated

The Ursinus Weekly, February 14, 1966

Happiness is the Lorelei: Traditional turnabout features peanuts, Whitians and kings • Dr. Riffe plans Shakespeare trips • St. Andrews Soc. offers stipend for study abroad • Agency Olatunji concert kicks off winter IF • Art is contemplation • Mrs. Pancoast to speak at Color Day • PSEA hears talk on ed. changes • Editorial: Situations to ponder • Controversy suggests student interest in local art exhibited in Wismer: What is it? they ask • Aching need filled by Supply Store a-go-go • Quiet hours shattered by fire as candle sets Hobson ablaze • Kersey lauds IF initiative • Paw prints • Intramural corner • UC dropped by E\u27town, routs Hopkins • Women\u27s JV wins opener • Bears outshoot PMC; Lose to Swarthmore: Troster paces Ursinus • UC student, Class of 1971, satires greatly organized Supply Store • Greek gleanings.https://digitalcommons.ursinus.edu/weekly/1216/thumbnail.jp

Understanding the users and uses of UK Natural History Collections

UK natural science collections hold over 137 million items, an unrivalled source of data about 4.56 billion years of planetary development and hundreds of years of biological change, including the differences made by humans — but the scientific, commercial, and societal benefits of these collections are constrained by the limits of physical access, and by highly fragmented digitisation efforts with less than 10% digitally available. Following work with Frontier Economics in 2021, which showed potential for £2 billion in benefits to the UK economy from digitising all UK natural science collections, in 2022–23 the Natural History Museum London worked, with analytical support from McKinsey and Company, to understand the impact of what has already been digitised and shared by UK natural science collections — what is the demand for these data, what are they used for, and how does this deliver efficient, effective and impactful research?This study focuses on usage via the Global Biodiversity Information Facility, the largest source of relevant usage data, examining 7.6 million records from twelve UK institutions. While these UK collections data are just 0.3% of total GBIF occurrences, they are cited in 12% of peer reviewed publications citing GBIF data, showing the disproportionate impact of UK collections data and the historical, geographical, and taxonomic richness that they bring. Researchers have already benefited from more than £18 million of efficiency savings from digital UK specimen data. Data from natural science collections held in the UK are uniquely impactful resources, vital to a future in which people and planet thrive, and a step change in the pace of digitisation is needed to unlock their potential for researchers, policymakers, and society