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Incyte Genomics to Sell Access to Proteome BioKnowledge Databases
Submitted by Martin Kucej; posted on Thursday, April 18, 2002 (14 comments)
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One of the most useful databases, which gathers comprehensive data on proteomes of several organisms, including yeast and human, will require a paid subscription as of June 1st of this year (2002).
Incyte Genomics plans to charge $2000 US per year per laboratory to access the library. A laboratory is defined to be ``a single Principal Investigator, his/her postdoctoral fellows, graduate students, and technical support (usually 5-8 individuals).'' According to information provided, ``larger labs, depending on their size, may be required to purchase multiple subscriptions.''
Charging the fee of $2000 US will simply mean cessation of its use for thousands of laboratories, mainly from poor countries, unfortunately, also including most of the European laboratories.
Incyte Genomics seems to take seriously its slogan: ``Integrating the Science and Business of Genomics.''
For more information:
http://www.incyte.com/sequence/proteome/subscription.shtml
http://www.incyte.com/sequence/proteome/faq.shtml#start
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Expanded view | Monitor forum | Save place
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What a total bunch of cowboys. When proteome.com was established, many accademics contributed on the understanding that this would be a free of cost free for all to use system and therefore forward scientific understanding and discovery.
I know many American labs are planning on boycotting the service (whether they go through with it though...) My lab certainly can't afford the fee. Can I get the information I have contributed to proteome removed? Or charge Incyte for it's use...??!!?
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As a graduate student about to start the writing up process, the construction of my thesis will be much difficult with out this valuable database. I guess I need to try and get as much done as possible before June 1st. I wonder how much paper it would take to print of the whole of the pombePD??!!!
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Well, I guess they'll block your access, when they find you are trying to do that. It happened to us, when we've been downloading "a lot" of information (we were analyzing DNA array results) they blocked our IP, and we had to ask them for access and explain why we were doing so much downloads. Now they'll be twice as carefull, I think.
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Private companies take granted that they have free access to public research achievements, but once they use it to find something out, it's immediately restricted. It was so much useful database... If you know about any initiative, please, post it here...
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Incyte
Submitted by Nobody; posted on Thursday, May 16, 2002
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Friends-
I haver a connection with Proteome/Incyte who intends to make sure that these comments are read. While many of us are disappointed in this decision, we need to try and be constructive to help Incyte decide how to best help us academics. If you have suggestions about how to lessen this impact, post them here. For example, it would be great if you could buy access to one database for substantially less money than access to all the databases, or perhaps if you could buy access for 24 hours.
I am hoping for a good turnout here, and to try and convince Incyte that this is a mistake that will damage many labs.
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Incyte
Submitted by Nobody; posted on Tuesday, June 04, 2002
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I am the pricipal investigator of a small academic lab (3 grad students and a postdoc) with not nearly enough research funding to pay $2000/year for a Proteome subscription.
I am suprised that it is legal for Incyte to resell the copyrighted data that we have generated. I have in fact contributed missing data myself in the past to WormPD, when it was publicly available.
It seems like Incyte will be creating a public relations fiasco by charging academic labs for use.
The institutional pricing structure will certainly need to be more explicit (the same way as journals charge for institutional use, for example) for academic libraries to be even capable of following up on it.
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Dear Gentleman,
metalife knowledgebase offers the user a ?single entry point? for research and analysis of available decentralized allocated data. metalife knowledgebase also increasingly integrates data that have been generated by means of own newly developed tools. for instance, by means of the text extraction tools and based on the metalife tmp (tmp = text minding process), data can be derived immediately from scientific publications and used for supplementation of annotations to protein entries or addition of new classes of information to the metalife knowledgebase. the metalife knowledgebase is based on standard components ( pc, sql server 2000). it contains the majority of public accessible molecular biological data as well as indices to the primary data collections, serves as a central in-/output memory for the metalife tools and applications, saves information and knowledge references that are created by highly developed metalife technologies, allows the easy integration of proprietary data and applications, compatible with internet technology. the metalife knowledgebase forms the fundament of our progressive bio-informatics package.
best regards
your Metateam
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Dear Gentleman,
In april 2002 the metalife team released the first version of the metalife explorer.
with metalife explorer the next central metalife tool is implemented in a first version. It enables the user to access the content of metalife knowledgebase thoroughly. All integrated data sources are exploited with one query. Simple queries as well as advanced queries are possible. The user does not need to know the internal data structures of the different data sources. Cross database queries are possible. A compact yet comprehensive dossier about a gene or a protein can be obtained with a single query. Data obtained from
structured databases stand in line with text extracted data. Among others, information of the dossiers includes sequences, pathways, publications, patents and relation to diseases. metalife explorer serves as a core part of the metalife working environment.
best regards
your Metateam
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Dear Gentleman,
Metalife finder offers, as an alternative to the user interface of metalife explorer, a classic search method. The tool is designed for those users who would purposefully like to access separate primaty data collections. By integrating the metalife working environment, an interface was created to all other applications.
The most important product features are:
? parser based user interface
? classic access to separate data collections
? based on the metalife knowledgebase
? possible inquiries about multiple databases and data categories
? integrated in the metalife working environment
best regards,
your metateam
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metalife bio explorer offers detailed information like, for instance, sequence homologies, regulation of gene expression, genorts, clones and their commercial availability, mutations, phenotype information, a complete description of the diseases associated with this gene, and as far as available, treatments and their biochemical background information. the program also serves as a compendium for all scientific publications to these categories and facilitates the fast and easy access to these publications. it also provides detailed information on proteins. a broad complete structural and functional classification, detailed data on domain structures and motive composition, on secondary structures and sub-cellular localization in relation with information on functional homologies of orthologisms and paralogs complete the information on protein functions and facilitate an overview of all common characteristics of proteins.
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the metalife viewer visualizes the data of the area of knowledge of life processes accumulated in metalife knowledgebase in order to facilitate the intuitive explication of biological processes. the user can search for network of molecular interactions, pathways, functional network or other ontology. metalife viewer contains a highly effective filter that gives the possibility to obtain reports with the required contents. in combination with additional processing algorithms data can be processed and sorted in appropriate order. this gives the performance to represent data visually, and form the searched knowledge to pass to hypotheses. metalife viewer can communicate and interact with all other modules developed by metalife.
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the metalife predictor is based on the up-to-date methods of top development and technologies for these purposes. various algorithms are used for improvement and mutual combinations in order to maximize the correctness of forecasts. discrete intrinsic molecular characteristics are used by these algorithms. the metalife predictor contains also internal "machine learning" algorithms for the formation of functional characteristics of biological objects. one of functions realized by metalife predictor is the use of sequence-based vector analyses in multidimensional frames. these self-learning algorithms are useful for the forecasts of protein-protein interactions, subcellular localization of either prokaryontic and also eukaryontic proteins as well as in ontology-based classification of proteins.
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The metalife validator combines the power of metalife predictor algorithms with internal basic information and the data of publications on knowledge of life processes or of other sources. This internal basic information will be processed by metalife analyzer and metalife generator, the results will be completed and ejected if they do not fit for the forecast, and in the context of internal basic information they will be processed and verified according to the normal way of checking and processing the accumulated information.
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metalife analyzer combines algorithms for the creation and improvement of knowledge-based ontologisms, for the promotion of lexical tools? development and for making the extraction of knowledge possible by means of automated classification and derivation of common concepts.
various internal implementation forms of metalife analyzer continuously feed the results in the metalife knowledgebase. metalife analyzer uses high-developed algorithms for semantic text analysis aimed at the classification of texts and establishment of their conception context.
for one of these algorithms, metalife tmp (text minding process), a patent application was placed on 06.07.2001 (no. 101 32 320.4) with the german patent office. the proprietary thesauri covering a full spectrum of various biological categories, as well as the extensive synonym and acronym lists and the further developed ontologisms represent important components of the metalife products.
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