A <i>Saccharomyces cerevisiae</i> Internet protein resource now available

Latter, G; Boutell, Thomas; Monardo, Patrick J.; Kobayashi, Ryûji; Futcher, Bruce; McLaughlin, Calvin S.; Garrels, James I.

doi:10.1002/elps.11501601193

Cited by 19 publications

(3 citation statements)

References 3 publications

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“…Since several reviews and books have recorded the major events which followed the appearance of high resolution 2-DE [ll-181, we will not review the development of this field in detail here. Enormous progress has been made in the development of databases for cells in culture [19,20], plasma [17,21,221, rat and mouse liver [23,241, heart tissue [25, 261, E. coli [27], and yeast [28], among others. Among the major technical advances has been the development of methods for identifying proteins from 2-DE gels by microsequencing and mass spectrometry [29][30][31], and of immobilized pH gradient electrophoresis as a practical tool to extend the pH range and improve reproducibility [32-341.…”

Section: Introductionmentioning

confidence: 99%

Twenty years of two‐dimensional electrophoresis: Past, present and future

Anderson

1996

Electrophoresis

183

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Section: Introductionmentioning

confidence: 99%

Twenty years of two‐dimensional electrophoresis: Past, present and future

Anderson

1996

Electrophoresis

183

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“…At the same time, the Internet provides a simple and efficient way to publish and share various sorts of data, and it has thus become necessary to follow a few standardization rules. From the point of view of 2-DE data, rules have already been proposed to build federated 2-DE databases [3], such as SWISS-2DPAGE at Geneva University Hospital [4,5], HSC-2DPAGE at Harefield Hospital [6], REF52 [7] and YEPD [8] at QUEST Protein Database Center, or HEART-2DPAGE at German Heart Institute Berlin [9]. A federated 2-DE database provides access to its own data set, through keyword search or spot clicking, but it also provides active links to other related servers.…”

Section: Introductionmentioning

confidence: 99%

Make2ddb: A simple package to set up a two‐dimensional electrophoresis database for the World Wide Web

et al. 1997

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Two-dimensional electrophoresis (2-DE) has become a highly reproducible protein separation technique that currently serves as the main basis for proteome research and in particular for protein identification. Also, the Internet provides large utilities for exchanging data, and we can observe increased interest among scientists to build remote 2-DE databases, since many members of the concerned community are now able to access the data. By preparing the data and programs that are required to create a federated 2-DE database, the Make2ddb package, described here, helps to build such a database on the user own World Wide Web site.

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“…[2] Genomics (species specific): DictyDb (Smith et al, 1997); EcoGene (Rudd, 2000); FlyBase (The FlyBase consortium, 1999); GeneCards (Rebhan et al, 1998); GeneCensus (Gerstein, 1998); HIV (Kuiken et al, 1999); HUGE (Kikuno R. et al, 2000); MaizeDB (Polacco et al, 1999); Mendel (Price et al, 2001); MGD (Blake et al, 2001); Micado (Perriere et al, 1999); NRSUB (Perriere et al, 1998); MIM (Wheeler et al, 2001); SGD (Ball et al, 2001); StyGene (Sanderson et al, 1995); SubtiList (Moszer, 1998); TIGR (Quackenbush et al, 2001); TubercuList (Cole, 1999); WormPep (Sonnhammer et al, 1997); YPD (Costanzo et al, 2001); ZFIN (Sprague et al, 2001 (Touzet et al, 1996); SWISS-2DPAGE (Hoogland et al, 2000); Aarhus/Ghent-2DPAGE (Celis et al, 1998); YEPD (Latter et al, 1995). [4] 3D structure: HSSP (Dodge et al, 1998); PDB (Bhat et al, 2001); PRESAGE (Brenner et al, 1999) SWISS-3DIMAGE (Peitsch et al, 1995).…”

Section: Explicit and Implicit Linksmentioning

confidence: 99%

SWISS-PROT: Connecting Biomolecular Knowledge Via a Protein Database

Gasteiger

Jung²,

Bairoch³

2001

Current Issues in Molecular Biology

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With the explosive growth of biological data, the development of new means of data storage was needed. More and more often biological information is no longer published in the conventional way via a publication in a scientific journal, but only deposited into a database. In the last two decades these databases have become essential tools for researchers in biological sciences. Biological databases can be classified according to the type of information they contain. There are basically three types of sequencerelated databases (nucleic acid sequences, protein sequences and protein tertiary structures) as well as various specialized data collections. It is important to provide the users of biomolecular databases with a degree of integration between these databases as by nature all of these databases are connected in a scientific sense and each one of them is an important piece to biological complexity. In this review we will highlight our effort in connecting biological information as demonstrated in the SWISS-PROT protein database. Data Integration Using Cross-ReferencesThe current situation of a research scientist has been described quite accurately by a quote from John Naisbitt, saying that "We are drowning in information, but starving for knowledge". The World Wide Web (Berners-Lee, 1999), which immensely facilitated information exchange between information providers and users, now offers the life science community a wealth of easily accessible knowledge and information. While clicking on hypertext links and thus navigating between databases maintained around the world seems to be a technically easy task, the challenge lies in extracting the complete and up-to-date information related to a research field from the hundreds of databases available. The user can be assisted in this task by the creators of information resources, who should attempt to provide a system that allows scientists to rapidly and efficiently consult all information pertinent to a given topic. This is usually done by establishing cross-references from each record in a database to related entries in other databases. (Bairoch et al., 2000) is a curated protein sequence database, which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications (PTM), variants, etc.), a minimal level of redundancy and high level of integration with other databases. Cross-References in SWISS-PROT SWISS-PROT SWISS-PROT Entry Format, a Sample Entry and Line Types Implementing Cross-ReferencesA SWISS-PROT entry is composed of different line types, and each line is introduced by a two-letter code indicating the type of data following on that line (see Figure 1 for a sample entry). The first section of every SWISS-PROT entry contains the entry name (ID), a unique primary accession number (AC), sometimes followed by several secondary accession numbers, and dates indicating when the entry was created and when its sequence and annotations were last updated (DT). The de...

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A Saccharomyces cerevisiae Internet protein resource now available

Cited by 19 publications

References 3 publications

Twenty years of two‐dimensional electrophoresis: Past, present and future

Twenty years of two‐dimensional electrophoresis: Past, present and future

Make2ddb: A simple package to set up a two‐dimensional electrophoresis database for the World Wide Web

SWISS-PROT: Connecting Biomolecular Knowledge Via a Protein Database

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