- What does BioCarta mean by an "open source" approach to biology?
- Why do you call BioCarta a "graphic database"?
- How can I participate in the Proteomic Pathways Project by submitting a new pathway or a modification to a current pathway?
- Who can be a Pathway Guru?
- What will I have to do as a Guru?
- What are the advantages of using the BioCarta Macromedia Freehand template to draw diagrams versus using the other templates provided (Adobe Photoshop, Adobe Illustrator, Microsoft Powerpoint), or drawing my own in another program (Canvas, MacDraw, etc.)?
- How do you ensure the material presented is not junk?
- Can I copy, download, or incorporate BioCarta diagrams into my own work?
- Is a contribution to BioCarta an on-line publication? What is the legal implication of submitting a pathway?
- Does Pathways list negative results to experiments?
- What if I want to Sponsor a pathway or advertise on this site?
- May I link my web page to a specific portion of the BioCarta site?
- Why would I submit a non-commercialized reagent to the BioCarta Reagent Exchange?
- Who is behind BioCarta?
- How is BioCarta funded?
- How can I draw my own pathways using the BioCarta master template?
- Will access to the BioCarta site remain free?
1. What does BioCarta mean by an "open source" approach to biology?
Though many companies and labs work to map gene product interactions, it is unlikely that their efforts will be comprehensive or prioritized by critical, disease-linked gene products. By working with the entire life science research community - 300,000 strong - to develop this content, BioCarta mimics the way OS programmers build an optimal Linux operating system. Our technology incorporates the input of each scientist from his or her particular niche into the all-inclusive model. In this way, the entire research community builds, updates and corrects the model, making it ever more informed and accurate.
2. Why do you call BioCarta a "graphic database"?
The maxim "a picture is worth a thousand words" greatly understates the scope of BioCarta's graphic depictions of molecular or cell-to-cell interactions. The quantity of information the drawings contain would take many pages to describe in text. In addition, each comprises several genes, so that only multiple entries would have housed written information. Depicting concepts graphically makes it easy for scientists to orient genes within their contexts.
3. How can I participate in the Proteomic Pathways Project by submitting a new pathway or a modification to a current pathway?
For information on how to contribute and also graphical templates used to assist in the creation of your contribution, visit The Pathways How To Section.
4. Who can be a Pathway Guru?
Pathway moderators ("Gurus") review new information as it is received. When BioCarta receives multiple pathways depicting similar information, we combine them into one pathway, time permitting. Gurus clarify the role of suggested modifications in a given pathway. Following this, technicians modify the pathway to reflect the latest findings.
BioCarta Gurus are experts in their area of research. If your credentials meet these standards, why not moderate pathway submissions and modifications? Benefits are numerous and include helping to increase and integrate knowledge related to your field. Please contact us at Guru@BioCarta.com for more information.
5. What will I have to do as a Guru?
As the recipient of comments, questions, and suggestions for updates from the community, you distinguish between those submissions that should be incorporated into your pathway as an accepted fact and those that should be tagged as speculative. You are entrusted with keeping your pathway up to date and integrating reasonable and interesting information. As you monitor discussion boards and field questions, you will find scientific discourse of a familiar nature, however the BioCarta interface minimizes the time expenditure.
6. What are the advantages of using the BioCarta Macromedia Freehand template to draw diagrams versus using the other templates provided (Adobe Photoshop, Adobe Illustrator, Microsoft Powerpoint), or drawing my own in another program (Canvas, MacDraw, etc.)?
BioCarta's template of molecular icons and cellular structures simplifies pathway drawing. Just open the template in a window on the desktop and open a blank page as well. To produce your diagram, merely copy appropriate icons from the template then paste them into your desired configuration on the new page. Of course, no one will be able to view your drawing unless you make it available on the BioCarta site, on your personal site, or in some other presentation. When you are ready to make your creation public, just send us a copy. After review, we will integrate it into the overall BioCarta model.
- Ease of use
- Automatic hyperlinks to genes
- Consistent visual look
- Faster posting to the BioCarta site
Sometimes a diagram submission indicates more information, perhaps by degrees of intricacy in protein substructure, than can be rendered using the current BioCarta template. In these cases, we accept your suggestions and update template with a more precise icon.
7. How do you ensure the material presented is not junk?
We present two levels of graphic information:
1) At one level anyone can post anything that seems remotely possible. The desire of a contributor to maintain credibility in the eyes of his/her peers helps to ensure the quality at this level, as it does at annual meeting poster sessions. The contributor benefits from receiving early feedback from the scientific community. And the community profits from viewing work in progress before peer-review and publication.
2) At the second level, BioCarta designates and maintains a series of common core pathways that are stringently reviewed by top Gurus. These are likely to be the most popular pathways. Information that is not yet meticulously reviewed has a speculative suggestion with arrows indicating its status. Just as a handful of reviewers attempt to maintain the integrity of material published in a journal, so will the Guru and the community, as whole, correct inaccuracies.
8. Can I copy, download, or incorporate BioCarta diagrams into my own work?
We encourage people to download, copy, and use the diagrams in any form. Just be sure to credit BioCarta. Please review the Terms and Conditions statement that our lawyers insisted we include on the site.
9. Is a contribution to BioCarta an on-line publication? What is the legal implication of submitting a pathway?
Though BioCarta is not technically an online publication, it serves the same purpose. By posting a pathway or suggesting a pathway modification, you make a contribution to a public record. Portions of this record are peer-reviewed by our Gurus. BioCarta inventories the dates comments, submissions and suggested modifications are made and the individuals who make them (provided they do not do so anonymously, which is their right). This bestows immediate credit for ideas in real-time, not after months of delay as with many printed sources. Thus, if you have made public a great idea long before it appears elsewhere, BioCarta documents that fact in our public forum for all to see.
A submission to BioCarta is the same as a public disclosure. Therefore, we ask submitter agreement with one of those click [I Agree]/[Do Not Agree] buttons. By agreeing, the submitter makes a public disclosure and gives BioCarta the right to modify and update the pathway (through the Guru process) as new information becomes available. In addition, the submitter gives users of BioCarta the right to download and use images for their personal or public use as long as they acknowledge the title of the original pathway (thus the submitter can be identified) and BioCarta as the source. If you have any concerns about any particular image as it is rendered, then let us know what you want changed on the diagram, and we will do so. Accordingly, we can avoid any copyright concerns. BioCarta must copyright the site and its content but will grant users of the site a right to use the material under the conditions stated above.
10. Does Pathways list negative results to experiments?
Absolutely! BioCarta believes this is a powerful feature of the Pathways. The data is open to comment from the entire community through the discussion boards and via links to specific arrows in the diagrams. Not only can people give supporting data. They can also present opposing data or ask for clarification. This online dialog overcomes the time constraints of traditional scientific literature. Whereas the hardcopy exchange can take years or expire from lack of follow-up publications, BioCarta is immediate. A speculative suggestion on the BioCarta site might accrue a number of comments such as "could not confirm/I need help in reproducing this study/Didn't work for me/Are you sure it isn't this artifact." Such dialogue alerts other interested scientists interested that the outcome is perhaps not as robust as originally suggested. Thus, researchers can avoid wasting time doing experiments that have already proved problematic.11. What if I want to Sponsor a pathway or advertise on this site?
11. What if I want to Sponsor a pathway or advertise on this site?
If you are a commercial supplier of reagents and services, please contact our marketing department at info@BioCarta.com for more information or visit our Sponsorship Opportunities section on this website.
12. May I link my web page to a specific portion of the BioCarta site?
Yes! BioCarta welcomes either individuals or companies who desire a quick link to a diagram representing their research. In many cases, disease-associated sites can benefit from a link in their text to related molecular models on the BioCarta site. Software packages for analysis of high-density array experiments also benefit from links to the BioCarta Gene Database. In so providing, they give their users the immediate ability to observe how a particular gene might interact with others, which might otherwise require exhaustive literature review.
13. Why would I submit a non-commercialized reagent to the BioCarta Reagent Exchange?
- As you published it, you are obligated to make it available. BioCarta handles the burden of acquiring import permits, packaging, shipping and charges. Before we ship, you review all requests. In cases of limited supply, we only ship to those you deem most qualified.
- Overstock may be valuable to someone else. This can be a way to kick-start collaborations.
- Reagents are a currency among researchers. Attaching any conditions to the listing, you control who gets your product and what you get in return. If you are willing to swap for only specific items from others, that's ok. If you are willing to donate it to others, that's great!
- Test the product demand before spending time to commercialize it through out-licensing.
- Attract companies who may wish to license and commercialize your product.
14. Who is behind BioCarta?
BioCarta originated with a group of scientists and engineers who recognized the constraints and obsolescence of hardcopy scientific literature. The pace and global nature of life science today need not suffer the delays of this antiquated communication medium, thanks to Internet technology. Since its inception, BioCarta continues to attract foresighted, energetic professionals. To learn more about our team, and about career and sponsor opportunities, please visit the About Biocarta Section
15. How is BioCarta funded?
We received an initial round of financing from New Taurus Ventures, in which Dr. Ernest Chun-Ming Huang (founder of PharMingen) is a major investor. We are currently pursuing another round of funding and exploring alliances with several key partners in the life sciences community.
16. How can I draw my own pathways using the BioCarta master template?
We encourage you to use the BioCarta templates. Our Macromedia Freehand 9.0 template has the following advantages:
- Easy-to-use molecular icons and cellular structures
- Automatic hyperlinks to genes
- Consistent visual look
- Faster posting to the BioCarta site
We have provided the template in earlier versions of Freehand as well as in Adobe Illustrator but NOTE that these do not contain the automatic hyperlinks to genes.
We are working on software that will allow you to use the template with only a web browser. This online drawing tool will be made available to all BioCarta users and will allow offline drawing as well. Register as a BioCarta member to receive notification when this tool will be ready for distribution.
To download and use BioCarta templates, click on Download Pathway Tools on the bottom of the main Pathways page.
17.Will access to the BioCarta site remain free?
The BioCarta Proteomic Pathway Project (P3) on the BioCarta web site aims to make sense of the numerous important molecular interactions that will be elucidated over the next several years as research efforts focus less on finding genes and more on finding out how gene products interact. Integrating and organizing this rising flood of proteomic information into a dynamic real-time on-line model that can catalog and summarize important findings is a main goal of the P3.
We believe that such valuable information, once publicly disclosed anywhere,
should be easily accessible for free to researchers, educators, and the
public everywhere. Therefore, BioCarta will never charge an access fee or
require registration to view information in this community resource.