Archive for category Community Building
Encouraging Collaboration in Washington as a Hub for Chemistry Databases
Posted by tony in Community Building, Computing, Data Quality, NPC Browser and NCGC Collection, Open Science..all its forms, Politics, Quality and Content on August 1, 2011
On August 25/26 I will be attending the 5th Meeting on U.S. Government Chemical Databases and Open Chemistry. I will have the opportunity to spend time with people I appreciate for the contributions they are making to chemistry: Martin Walker, JC Bradley, Andy Lang, Markus Sitzmann, Ann Richard, Frank Switzer, Evan Bolton, Marc Zimmermann, Wolf Ihlenfeldt, Steve Heller, John Overington, Noel O’Boyle, and many others. It is surely going to be an excellent meeting. The agenda is given here.
Some of the people listed above are associated with “Washington-based databases”. Databases that are developed in or around Washington by government-funded organizations – the FDA, NIH, NCBI/NLM, NCI, NIST. There are also other government funded databases, non-Washington-based, represented – EPA and CDC. If you are not sure what all those three letter acronyms are then here you go.
FDA – Food and Drug Administration
NIH – National Institutes of Health
NCBI/NLM – National Center for Biotechnology Information/National Library of Medicine
NCI – National Cancer Institute
EPA – Environmental Protection Agency
CDC – Center of Disease Control
NIST – National Institute of Standards and Technology
One organization with a chemistry database conspicuous by its absence is the NCGC data collection contained in the NPC Browser. I’ve blogged a lot about this one on this blog.
NCGC – NIH Chemical Genomics Center
I am hoping to get to talk to some members of the team if they attend the meeting though.
There will be a LOT of government databases represented at this meeting. I have experience with many of the databases provided by these institutions. The DSSTox database is one of the most highly curated databases based on my review of the data. The NCI resolver is an excellent resource with good quality data in terms of the accuracy of name-structure relationships.
The various databases are developed independently of each other. True, some of the databases contain contents from some of the other databases but, as far as I can tell, there is not much collaboration in terms of coordinated curation of data. What would it be like if each of these organizations participated in a roundtable discussion to agree to a process by which to collaboratively validate and curate the data, once and for all? Maybe this meeting can catalyze such a discussion. I would encourage the organizations to take advantage of other data sources that can share their data – ChEBI/ChEMBL is one example! If these various groups coordinate their work then the result could be a massively improved quality dataset to share across the databases and across the community. If this work was done then the group that assembled the NPC Browser would likely have a lot less work to do in terms of assembling the data. The various database providers should certainly have provided clean, curated data for many of the top known drugs. While working on a manuscript reviewing the quality of public domain chemistry databases I assembled a table of 25 of the top selling drugs in the US and checked the data quality in the NPC Browser relative to a gold standard set. The assembly of the data will be discussed in its entirety in a later publication.
25 of the Top Selling Drugs in the USA - Data Quality in the NPC Browser
The errors listed in the table are:
1 Correct skeleton, No stereochemistry
2 Correct skeleton, Missing stereochemistry
3 Correct skeleton, Incorrect stereochemistry
4 Single component of multicomponent structure
5 Multiple components for single component structure
6 No structure returned based on Name Search
7 Incorrect skeleton
8 Multiple structures based on name search
Clearly there are a lot of errors in the structures associated with 25 of the best selling drugs on the US market. These should be the easy ones to get right as they are so well known!!! Collaboration between the domains top database providers would have helped, almost certainly. This would not necessarily be an issue of meshing technologies but agreeing on a common goal to have the highest quality data available. Since the government puts so much money into the development of these databases it would be appropriate to have some oversight and push for aligning efforts. Collaboration is essential!
With that in mind…a shameless pointer to how Sean Ekins, Maggie Hupcey and I BELIEVE in the need for collaboration…our book. If we can encourage others in the government chemistry databases to adopt active collaborative approaches wonderful things could happen.
Collaborative Computational Technologies for Biomedical Research
Announcing the SciMobileApps Wiki for Community Based Listing of Science Apps
Posted by tony in Community Building, Computing, SciMobile Apps Wiki on June 21, 2011
I am sure that most of you are already smartphone or tablet users as many people visiting this blog are, like me, interested in the latest technologies. I’ve been a smartphone user for a number of years and certainly did get caught up in the iPhone and iPod wave using both mobile technologies. Now with the Android OS abounding on both phone and tablet it will be interesting to see how the next few years play out for me in terms of dedication to Apple technologies.
With the “world of Apps” came a lot of interest in how science would make use of this new technology platform. I have given presentations on “Mobilizing Chemistry” and it has had over 3000 views. I’ve written an article with Harry Pence regarding SmartPhones in the classroom and have been very passionate about making sure that ChemSpider is supported on mobile platforms with ChemMobi [Working with James Jack 1,2] as well as the Mobile Browser support work done by Sergey Shevelev in our team [3,4]. While my personal bias is chemistry clearly apps cover all of science….and these scienceapps are growing in number.
I am fortunate to have worked with a terrific group of co-authors to pen an article regarding “Mobilizing Chemistry in the World of Drug Discovery”. This article, written by Sean Ekins, Alex Clark, Rich Apodaca, James Jack and myself was submitted today. In parallel Sean and I decided that since we had done the work to assemble a collection of apps for the article it made total sense to keep track of this on an ongoing basis so we’ve set up a wiki so that the community can help us track what is available. This wiki is at www.SciMobileApps.com and offers you the opportunity to update the wiki with an overview of a scientific app or your review of an app that might already be there. Wikipedia is very cautious about having articles posted on apps as they see them primarily as advertising. We are of the opinion that this site can serve the ability of advertising your apps if you are willing to put in the work to list it. As long as you do this in an appropriate manner, much as emulated by Alex Clark with his MMDS, MolPrime, Yield101 and Reaction101 apps, there is no problem.
It is assumed that most of you will know how to edit in the world of MediaWiki. If not I suggest looking for basic MediaWiki instructions online (it’s the same platform as used for Wikipedia!). As you will see the SciMobileApps is NOT just for chemistry but for all forms of science as listed on the Main Page and can even be extended as the community sees fit. As time allows we’ll put together a page of help tips for you to follow and maybe a short movie. This is an after-hours project only and is aligned with the publication we have submitted for publication. This is simply a community resource for scientists. Enjoy. We welcome your feedback.
Integrating and Curating Internet-Based Chemistry Resources to Serve Life Scientists
Posted by tony in ChemConnector, ChemSpider Chemistry, Community Building, Publications and Presentations, Quality and Content on June 15, 2011
Speaking at the ORCID Meeting Next Week
Posted by tony in Community Building, Publications and Presentations on May 13, 2011
I will be presenting at the ORCID Meeting in Boston next week (Wednesday May 18th). If you are interested in attending in person or virtually, please register here . The meeting is co-sponsored by the Harvard Office for Scholarly Communication, and the Harvard Institute for Quantitative Social Science, and the Harvard Office of the Provost.
Date and Time
May 18th, 2011
9:00 AM through 5:00 PM
Location
Tsai Auditorium, CGIS Building
Harvard University
1730 Cambridge St.
Cambridge, MA 02138
Webcast
Those unable to attend in person can follow via the live webcast from 9 AM to 5 PM at with broadcast audio and viewing of the presentation slides.
Program
9:00 Welcome
9:10 Howard Ratner, Organization Update
9:30 Amy Brand, Business Working Group
9:50 Brian Wilson, Technical Working Group
10:10 Martin Fenner, Outreach Working Group
10:30 Coffee Break
11:00 Howard Ratner, Discussion ORCID Organization
11:30 Ferdi Alimadhi, Harvard University and OpenScholar
12:00 Lisa Schiff, California Digital Library (CDL)
12:30 Gregg Gordon, SSRN
1:00 Lunch
2:00 James Robert Griffin III and Thomas Krichel, Open Library Society
2:30 Micah Altman, Harvard and Dataverse
3:00 Todd Vision, NESCent and Dryad
3:30 Break
3:45 Tony Williams, ChemSpider and Royal Society of Chemistry
4:15 Gudmundur Thorisson, Leicester University
4:45 Martin Fenner, Discussion Data Citation and ORCID
5:00 Howard Ratner, Closing Remarks
The abstract for my talk is as follows:
ChemSpider is one of the world’s primary internet resources for chemists and is a crowdsourcing environment where users can deposit, annotate and validate data. What Wikipedia is to encyclopedic articles ChemSpider intends to be for chemistry-related data. Since scientists contribute their time, data and expertise to enhance the content and quality of the database we intend to develop a rewards and recognition system. Ultimately measures of contribution should feed an alternative metrics platform for community recognition. A researcher identifier, such as that encouraged by ORCID, would underpin this work. This talk will provide examples of ChemSpider contribution and how ORCID would be used.
Calculating my H Index With Free Available Tools
Posted by tony in Community Building, General Communications on April 23, 2011
In a conversation this week I was asked what my H-Index was. It is regarded as a measure of the impact of the published work of a scientist and after 20 years of publishing I am interested in how the work I have been doing for the past two decades is received.
I’m not going to discuss in detail some of the views of the H-Index measure as this has already been done on a number of blogs (1,2 and 3). Rather, I am going to see what freely available tools I can use to compute my H-Index. There are numerous ways to generate the H-index including the Google Scholar Universal Gadget, the Publish or Perish desktop software and the Scholar H-index Calculator.
Using each one at a time…
The Scholar Gadget
1) The Google Scholar Universal Gadget is EASY to use. I inserted my name as shown below and was given the statistics shown. I have over 100 peer-reviewed publications listed in my CV so 55 is pretty low. Clicking on the “view publications” gave me 83 listed in the Google Scholar search. Certainly not all of my publications are listed. The highest number of citations is 48 for a paper I was involved with at Kodak but there are a number of fairly well cited papers.
2) The Publish or Perish software was downloaded and installed in a couple of minutes. It was fairly obviious how to use it and within a few minutes I had pruned the retrieved hit list of articles down to those I had authored or co-authored. The resulting statistics are shown below. In this case I am associated with 65 papers giving an H-index of 15 and published over 22 years. Many of my papers are missing but the H-index is similar to that determined by the Google gadget. The various other statistics are not something I understand yet but will be looking into. While the Publish or Perish is very powerful (especially the formats it will allow me to save the stats out are very flexible and complete) it is probably a little too much for someone just looking for a “number”.
Publish or Perish Desktop Software
3) The Scholar H-index Calculator is an Add-on for Firefox from Agelin Bee. This add-on utilizes the Google API in the same way that the Google Gadget does but offers the ability to prune the data through an advanced interface integrated to Firefox. This approach ultimately gave the same H-index of 16 from the other gadget, not unexpected since it is using the Google API, and uses 83 publications, even after pruning. Overall this was my PREFERRED tool for finding an H-index value. Is it correct? I don’t know. But three tools seem very consistent yet don’t seem to be retrieving all of my publications…and one would assume those they can’t find might not be highly cited!
The Firefox Google Scholar Add-in
Just_out_of interest, the list of living chemists with an H-index>50 is pretty long. I have not worked in academia since 1990 when I worked at the University of Ottawa as their NMR Facility Manager. I am fortunate to have continued a scientific career enabling me to publish “after hours” and I don’t foresee me hitting the “50s” anytime soon! I am interested to know how the H-index generated with free online tools compares with commercial tools. I also hope to do some examination of the contribution of “old” articles to the H-index as there are a number of articles from early in my career that seem to have 0 citations and I know they were cited. It appears that many of the more recent articles have citations though. So, I wonder whether the presence of an article in the digital work is contributing some form of bias? This is just perception at present….
Drugs, Racemic Mixtures, Data Curation and Tautomers
Posted by admin in Chemicals and our Health, Community Building, Data Quality on February 9, 2011
Yes, that’s quite a title for a blog post. But it covers the nature of exchanges that Egon Willighagen and I have been having recently (that among others as we are co-authoring a book chapter on Computational Toxicology also). Egon asked a question on the Blue Obelisk Discussion group about tautomers and I answered it on this blog. Egon has posted a follow up blog post here. His most recent post makes a series of valid comments…all good and well worth discussing.
Egon then asked about one of the compounds on ChemSpider here saying
“Anyway. Tautomerism was a curation issue in the first(!!!) entry I was curating. The sixth had the more well-known problem, I think. I may be blind, but I would say this drug has a stereocenter:
But none of the databases I checked so far (including ChemSpider) defines the stereochemistry! I thought we settled that some decades ago? Stereochemistry of drugs matter. What is going on here?”.
The drug shown is Aminoglutethimide. It’s on Wikipedia here without specific stereochemistry. But as we know Wikipedia does have errors (see slide 47/126 here). So what gives? It’s on KEGG in the same way. Also on ChEMBL here. But it IS on ChemSpider as both stereoforms….R and S. I would suggest that the drug is likely a racemic mixture of the stereoforms and as represented on all of the databases it’s probably okay to not draw the stereobonds as there is only one stereocenter to worry about. Checking Dailymed supports this in this record. A search on “Aminoglutethimide” gives 36000 hits on Google…I did not wade through them! I think the drug is therefore supplied as a racemate, can be separated (see top google hits) but is okay on ChemSpider as is.
The Day I Noticed that CAS SciFinder Now Supports #InChI
Posted by admin in Community Building, Data Quality, InChI on February 8, 2011
Today. Today is the day I noticed that CAS Scifinder now supports InChI! Wow. Now, that may not be big news for many of you but for those of us who have supported InChI, both vocally AND in action around it, this is big news. InChI is not perfect and has areas to develop in (some later posts will cover this) but it is ALREADY extremely enabling. (For an example about InChI issues…but focused primarily on how people DRAW structures that they feed to InChI algorithms see slides 75-84 on this presentation http://tinyurl.com/4hhgqbd)
It is helping to link databases, enable web searching and improve communication between cheminformatics applications. ACS and CAS have been quite late in providing support for InChI and today I noticed it has arrived. This is great news for InChI and very much a blessing for InChI as a standard for interchange. Now, if we can get StdInChIKeys layered onto all ACS publications then the need for an InChI Resolver will be increased….
Who Could Participate in #NMRCAVES
Posted by admin in Community Building, Computing, Nuclear magnetic resonance, Open Science..all its forms on January 20, 2011
I recently posted about the project that will become known as NMRCAVES, NMR Computer-Assisted Verification and Elucidation Systems. This will be a workshop to be held at SMASH. There will be no workshop without two essential ingredients: participants and data.
The participants will need to be willing participants to work with us with their software, algorithms and approaches to test their systems on data. The data will be data supplied by the community and provided to the participants in a blind study to test their systems.
To populate the workshop is the first challenge. if we cannot get enough participants then even though we might get an abundance of data there will be no workshop to hold if we cannot engage the groups to work with it. There are a limited number of groups/individuals working in the areas of computer-assisted structure verification and elucidation by NMR. I have listed them below. No offense meant if I have accidentally missed anyone out. Also, they are listed in alphabetical order so no favoritism either…
Verification
ACD/Labs Structure Verification with NMR Predictors
Bruker Complete Molecular Confidence
Mestre Labs MNova
Sciencesoft VerifyIt
Elucidation
ACD/Labs Structure Elucidator
Jmnsoft LSD
SENECA - package for Computer Assisted Structure Elucidation (CASE) ported into the CDK
Sciencesoft AssembleIT
Can anyone point me to groups or software solutions that I am missing and other potential solutions out in the community that I should approach? I will be approaching the listed groups with an invite to participate in NMRCAVES and then will be asking the community if you are willing to provide data for the project!
#NMRCAVES is NMR Computer Assisted Verification and Elucidation Systems
Posted by admin in Community Building, Computing, Data Quality, Nuclear magnetic resonance, Open Science..all its forms, Software on January 18, 2011
I am honored to have been invited to lead a workshop at the SMASH NMR conference later this year. I will be co-hosting with Michael Bernstein, someone who I have known for many years and with whom I have spent many hours (if not days!) discussing the ins and outs of NMR prediction and structure verification by NMR,
The workshop will provide an environment for developers of software packages and associated algorithms allowing for structure verification and elucidation to engage with interested members of the NMR community attending the SMASH NMR meeting. Presenters may include both commercial and non-commercial software packages and the workshop will allow the participants to report on their respective approaches as well as report on the performance of their algorithms against a large set of data provided by the community.
The one day workshop will be separated into Structure Verification and Structure Elucidation segments with participants who have chosen to participate in the project. We are hoping for participants from both the academic and commercial sectors.
I’ve called the workshop NMRCAVES: NMR Computer Assisted Verification and Elucidation Systems. Below is an outline to initiate a conversation with interested parties. It is a suggested outline for the project and I welcome feedback.
The data analysis components of the workshop are outlined below.
CASV: Four sets of data will be made available to the participants.
(1) HNMR only, minimum of 25 spectra and 25 suggested structures (random distribution of correct/incorrect with at least 50% correct)
(2) HNMR and 2D HSQC, minimum of 25 spectra and 25 suggested structures (random distribution of correct/incorrect with at least 50% correct)
(3) HNMR only, minimum of 25 spectra and 25 sets of 3 structures (1 of each of the 3 is the always the correct structure)
(4) HNMR and 2D HSQC (preferably multiplicity edited-HSQC) minimum of 25 sets of spectra and 25 sets of 3 structures (1 of each of the 3 is the always the correct structure)
The participants will receive the data via download from an FTP site with each folder numbered in an ambiguous manner. All structures will be known to only two parties: the laboratories acquiring the data and the host of the workshop (AJW). The participants will have the responsibility to provide a report identifying the correct/incorrect structures in test sets (1) and (2) and identifying the correct structure out of the combination of 3 provided in (3) and (4). When all reports have been submitted each participant will receive a report identifying the correct structures for their review and in order for them to report on their successes and to further review and report on the data during the workshop.
The overall performance statistics comparing the results of the various participants will be reviewed and presented at the workshop by the workshop host.
CASE: The objective should be to test the ability of algorithms to correctly elucidate the skeletons of unknowns with the provision of “high-quality datasets” where sensitivity is deemed not to be a limitation. While it is acknowledged that sensitivity is an issue in CASE approaches this particular hurdle should be removed from the challenging of the algorithms. Request data from a series of laboratories. The minimum dataset should include “High-resolution MS”, 1H, COSY, HSQC/HMBC. Additional data can include TOCSY, DEPT-HSQC, HSQC-TOCSY, 1H-N15 direct and long-range correlation, NOESY/ROESY.
The participants will receive the data via download from an FTP site with each folder numbered in an ambiguous manner. All structures will be known to only two parties: the laboratories acquiring the data and the host of the workshop (AJW). All elucidations will be done blind and the participants will have the responsibility to provide a report including a table of the top 3 structures for each dataset, rank-ordered if possible, from most-likely to least-likely. When all reports have been submitted each participant will receive a report containing the correct structures for their review and in order for them to report on their successes and to further review and report on the data during the workshop.
The overall performance statistics comparing the results of the various participants will be reviewed and presented at the workshop by the workshop host.
Outcome of Project
1) A review of the state of contemporary computer-based structure verification and elucidation
2) All data to be publicly shared and made available as Open Data for download and to become a gold standard reference set of data for the community to utilize for further testing and development
3) All processed spectra to be uploaded and available on a public domain database (e.g. ChemSpider) and associated with the correct chemical structure
4) A minimum of one co-authored publication reviewing the results of the workshop and associated studies
Your feedback, comments and questions are welcomed. We are especially looking for laboratories who are willing to provide sets of data for analysis during the project as well as software groups who develop algorithms for structure verification and elucidation and who wish to participate in the project.
Community Views and Trust in Public Domain Chemistry Resources
Posted by admin in Community Building, Data Quality on December 11, 2010
Over the past 4 weeks I have been involved with some new and old friends in the world of chemistry to initiate an analysis of “quality” in public chemistry resources. This is work in progress and involves 3 separate groups (lets call them labs) looking at various resources. Here’s s short description of the project.
The questions we are attempting to answer are:
Core question : what is the quality of data online in public chemistry databases? How accurate and unambiguous is the representation of chemical structures and their measured properties in public chemistry databases?
We’ve started with the top 200 selling drugs. The three labs had to come to an agreement about which of the top 200 drugs were small molecules (many of the top 200 are monoclonal antibodies or polymers for example). We then had to decide would we deal with mixtures and combination drugs. Just to identify the list of NAMES of drugs we wanted to deal with was iterative and a negotiation.
Then we decided that each lab would work independently, each lab would have at least two members of the lab working on the same problem independently. We would have both intra-lab and inter-lab comparisons. We decided to start on a set of 10 drug names, using the GENERIC name as the name to work from. I started my part of the work just before I had to give a presentation at the EBI last week and was able to gather a lot of the data before the talk.
Starting with a chemical name how to you determine what the “correct” structure for that drug is. Think it’s easy? Try it! Where would you look? How would you confirm? What would the iterative loop look like in order for YOU to assert the chemical structure(s) for the drug “Vytorin”.
For me the process looks something like this. Use a level of “trust and experience” with previously used resources as a starting point and declare “This is the structure of X based on searching on the drug name for X”. Now, cross-reference, iterate, reiterate, find consistencies and collisions in order to come up with a final assertion, a list of consistent structures and the associated sources, and a set of other resources with inconsistent structures and a list of why they differ. Where possible, and if necessary, make edits to change the information (e.g. ChemSpider and Wikipedia). You can see an example of this for Vitamin K in the talk I gave at EBI here. For ten structures I came up with a number of observations for a number of drugs. The screenshot below summarizes some of the results (Click on the image to see the detail).
Represented in the table is the following information, true at the time of the search and may be already out of date
1) A search for thalidomide in ChEBI gives no hits
2) The structures of Zocor and Crestor on Drugbank are incorrect
3) There are no hits for Voglibose and Crestor on Common Chemistry
4) There were 3 incorrect structures on ChemSpider (now edited of course)
5) For most searches on a drug name on PubChem there are MULTIPLE hits and, for the set examined, the correct structure is in the results set. For example, there are 44 structures of Taxol retrieved with the search and the one I assert to be correct is there.
6) There were two incorrect structures on Wikipedia and one drug without an associated structure.
When I started the work I had a “trust” level for a number of the databases. My basic position at that time was as follows. I could rarely find the correct structure for a drug based on a text-based search of PubChem. I would generally find a set of hits and it was a lot of work to determine what was correct. Common Chemistry was excellent…but limited. Dailymed was generally good but structure representations could be abysmal. ChEBI, DrugBank, ChemIDPlus and Wikipedia were generally VERY good. Of all of the sources I used, despite the rich data on PubChem, I struggled most with this resource to find the correct structure. The results started to show that my trust perceptions were being challenged.
In parallel with the work to prepare this small dataset for the presentation at EBI I decided that it was appropriate to ask the community for their views on some of the databases I was looking at in this work…specifically asking for how much they “trusted” a resource. Trust means different things to different people. The word, and the question I was asking in the survey, would be interpreted in different ways. But that’s the way we work…so why fight it? The survey is online here…and if you haven’t filled it in PLEASE DO!
The answers to date, from the 46 responders, are below (Click on the image to see the detail):
There are some very interesting results in here…and, I willingly admit, some I find VERY surprising. 1 person has no experience with Wikipedia? Wow. The majority of people have not heard of PDSP, ChemIDPLus, DailyMed or DrugBank…without knowing who the people are that are providing feedback of course I should not be shocked. Most of these resources are not for chemists per se but for Life Scientists. The number of votes for “Always Trust” for ChemSpider and PubChem are very high, and one might say, are a compliment. The results are clearly ChemSpider-biased since I asked the question to my social network. The difference between the people who Always Trust PubChem and Commonly Trust PubChem is one person only. This is wildly different from my own views. I have heard people say that PubChem is the equivalent of quality to CAS except it’s free. Sorry folks…afraid not! (I have since heard at the EBI meeting from one of the people from PubChem that it is possible to do searches in certain ways to limit hits. It should be noted that this does not guarantee that the correct structure is retrieved.) On the flip side to this the distribution of people rarely trusting PubChem is also quite high so someone has had some interesting experiences!
There are a small number of people who NEVER Trust the resources, and early on one person declared they trusted none of them. I trusted myself to tell a colleague…that will be “Egon Willighagen” and this was later confirmed in his blog “Trust has No Place in Science“. That may be true, and the topic of a separate post, but my judgment is pretty good!
How would I fill in the questionnaire. I would NEVER flag “Always Trust” for any of the databases. I would be able to rank order the databases in terms of my perceptions/experience and extracted trust for the quality of results I would find. The answers WOULD be different before I had conducted the work on the first 10 drugs compared with now, after the pre-work.
As the host of ChemSpider I would prefer that no one “Always Trusts” the resource as that will stop people from taking care with the data and thereby removing the possible value of them curating the data. However I am more than happy to have it Commonly Trusted and we have been working hard to gain the community’s trust in this area.
This work has triggered a number of responses….I’ll make my own comments on their positions separately… but their opinions are worth reading:
Egon Willighagen: Truth has no place in Science
Egon Willighagen: Truth has no place in Science Part 2
Christina Pikas: The role of trust in science Christina has a comment “I think that Anthony (sp.) could have chosen a better word than trust in his survey. “which of these have you evaluated and decided you could use? which of these would you prefer to use based on your evaluations of their merit?” Christina is right..I could have chosen a different word but I judge (chosen carefully!) that the responses would not have differed much.
There is also a healthy exchange happening on Friendfeed.
This work has only just started. An examination of >150 “small molecule drugs” by three labs is going to provide a lot of data. The work isn’t over and we have much to do. We’re learning a lot in the process about assertional loops, iterative process, collaboration and agreement. It’s a great adventure.