Egon Willighagen, 24/02/2015 | Source: chem-bla-ics
Egon Willighagen, 11/01/2015 | Source: chem-bla-ics
The first team (Mischa-Alexander and Hamza) focused on the ACE inhibitors (type:"drug class") and the WP554 from WikiPathways. The use a tree structure to list inhibitors along with their activity:
The source code for this project is available under a MIT license.
The second team (Catherine and Moritz) looked at compounds hitting diabetes mellitus targets. They take advantage from the new disease API methods and first ask for all targets for the disease, and then query for all compounds. Mind you, the compounds are not filtered by activity, so it mostly shows interactions that real targets.
This product too is available with the MIT license.
The third project (Nadia en Loic) also goes from disease to targets and they looked at tuberculosis.
Egon Willighagen, 09/01/2015 | Source: chem-bla-ics
- "The Royal Society of Chemistry has announced that it is donating 100 “RSC Gold” accounts – the complete portfolio of their journals and databases – to be used by Wikipedia editors who write about chemistry. The partnership is part of a wider collaboration between the Society’s members and staff, Wikimedia UK and the Wikimedia community. The collaboration is working to improve the coverage of chemistry-related topics on Wikipedia and its sister projects."
- Can you elaborate on the conditions? Is it limited to wikipedia.org or does it extend to other Wikimedia projects, like Wikidata? Does the agreement allow manual lookup of information only, or does it allow text mining on the literature as well as on the database? How should I put this in perspective with the UK law that allows text mining, and, in particular, can UK Wikipedia editors use text mining anyway, or is that restricted? Is there an overview of the details of what is allowed and not allowed, or a list of restrictions otherwise?
Egon Willighagen, 21/12/2014 | Source: chem-bla-ics
Egon Willighagen, 06/12/2014 | Source: chem-bla-ics
|Altmetric.com score for the news|
item by Van Noorden (see text).
Thanks to Altmetric.com (a sister company of ReadCube) and the DOI we can easily find all discussion around the news item by Van Noorden (doi:10.1038/nature.2014.16460) in blogs. From the free, open dissemination of scientific knowledge ideal point of view the product is limited:
- Is Nature’s “free to view” a magnanimous gesture or a cynical ploy?
- Nature’s Beggar Access
- Nature Free to View is Not Open Access
- Nature's ShareWare Moment
- Why ReadCube is DRMed and unacceptable for science
- Nature Opens the Archives
- Artikelen uit Nature mogen voortaan gratis gedeeld worden (Dutch)
- many, many more...
@egonwillighagen good question. a new use case we hadn't explicitly thought thru (have been as few - this really is an experiment!)
— Nature Publishing Gp (@npgnews) December 5, 2014
KDE's Konqueror). But clearly it is your browser that does the rendering. Therefore:
- you do download the paper
- you can copy the content (and locally save it)
- you can print the content
Egon Willighagen, 16/11/2014 | Source: chem-bla-ics
The Open PHACTS API support various formats and this JSON is the default format used by the ops.js library. However, the amount of information returned by the Open PHACTS cache is complex, and generally includes more than you want to use in the next step. Therefore, it is needed to extract data from the JSON document, which was not covered in the post #10 or #11.
Let's start with the example JSON given in that post, and let's consider this is the value of a variable with the name jsonData:
"tags": [ "Bar", "Eek" ],
For example, to get the price value from the above JSON code, we use:
var price = jsonData.price;
Or, if we want to get the first value in the Bar-Eek list, we use:
var tag = jsonData.tags;
Or, if we want to inspect the warehouse stock:
var inStock = jsonData.stock.warehouse;
Now, the JSON returned by the Open PHACTS API has a lot more information. This is why the online, interactive documentation is so helpful: it shows the JSON. In fact, given that JSON is so much used, there are many tools online that help you, such as jsoneditoronline.org (yes, it will show error messages if the syntax is wrong):
And with a JSON viewing extension, opening this https://beta.openphacts.org/1.3/pathways/... URL in your browser window will look something like:
var pathwayCount = jsonData.result.primaryTopic.pathway_count;
Egon Willighagen, 16/11/2014 | Source: chem-bla-ics
While there are full debugging tools, achieving the task of finding where the bug is can often be reached with simpler means:
- take notice of error messages
- add debug statements in your code
- find where the problem is
- try to solve the problem
Programming in the Life Sciences #18: Molecular weight distribution of compounds with measured activities against a target (and other examples)
Egon Willighagen, 16/11/2014 | Source: chem-bla-ics
Examples? A politician that actually lives in a neighborhood where he develops policies for. A principle investigator that tries to reproduce an experiment himself from one of her/his postdocs or PhD students. And, of course, the programmer that should use his own libraries himself.
Dogfooding, however, is not the single solution to development; in fact, it can be easily integrated with other models. But it can serve as an early warning system, as the communication channels between you and yourself are typically much smaller than between you and the customer: citizen, peer reviewer, and user, following the above examples. Besides that, it also helps you better understand the things that is being developed, because you will see factors that influence in action and everything becomes more empirical, rather than just theoretical ("making money scarce is a good incentive for people to get of the couch", "but we have been using this experiment for years", "that situation in this source code will never be reached", etc).
And this also applies when teaching. So, you check the purity of the starting materials in your organic synthesis labs, and you check if your code examples still run. And you try things you have not done before, just to test the theory that if X is possible, Y should be possible too, because that is what you tell your students.
And compared to last year when only the source was available, all these examples can now be tested online on the following GitHub pages (using their brilliant gh_pages system):
- Example 1: simple example where the Open PHACTS Identity Resolution System (name to identifier) system is used
- Example 4: uses d3.js to show a bar plot of the number of times a particular unit is used to measure activities of paracetamol
- Example 5: the same as example 3, but then as pie chart
- Example 6: the above molecular weight example
Egon Willighagen, 05/11/2014 | Source: chem-bla-ics
|Data needs for answering the scientific questions. From|
the paper discussed in this post (Open Access).
- Give me all oxidoreductase inhibitors active <100 nM in human and mouse
- Given compound X, what is its predicted secondary pharmacology? What are the on- and off-target safety concerns for a compound? What is the evidence and how reliable is that evidence (journal impact factor, KOL) for findings associated with a compound?
- Given a target, find me all actives against that target. Find/predict polypharmacology of actives. Determine ADMET profile of actives
- For a given interaction profile – give me similar compounds
- The current Factor Xa lead series is characterized by substructure X. Retrieve all bioactivity data in serine protease assays for molecules that contain substructure X
- A project is considering protein kinase C alpha (PRKCA) as a target. What are all the compounds known to modulate the target directly? What are the compounds that could modulate the target directly? I.e. return all compounds active in assays where the resolution is at least at the level of the target family (i.e. PKC) from structured assay databases and the literature
- Give me all active compounds on a given target with the relevant assay data
- Identify all known protein–protein interaction inhibitors
- For a given compound, give me the interaction profile with targets
- For a given compound, summarize all ‘similar compounds’ and their activities
- Retrieve all experimental and clinical data for a given list of compounds defined by their chemical structure (with options to match stereochemistry or not)
- For my given compound, which targets have been patented in the context of Alzheimer's disease?
- Which ligands have been described for a particular target associated with transthyretin-related amyloidosis, what is their affinity for that target and how far are they advanced into preclinical/clinical phases, with links to publications/patents describing these interactions?
- Target druggability: compounds directed against target X have been tested in which indications? Which new targets have appeared recently in the patent literature for a disease? Has the target been screened against in AZ before? What information on in vitro or in vivo screens has already been performed on a compound?
- Which chemical series have been shown to be active against target X? Which new targets have been associated with disease Y? Which companies are working on target X or disease Y?
- Which compounds are known to be activators of targets that relate to Parkinson's disease or Alzheimer's disease
- For my specific target, which active compounds have been reported in the literature? What is also known about upstream and downstream targets?
- Compounds that agonize targets in pathway X assayed in only functional assays with a potency <1 μM
- Give me the compound(s) that hit most specifically the multiple targets in a given pathway (disease)
- For a given disease/indication, give me all targets in the pathway and all active compounds hitting them
Egon Willighagen, 25/10/2014 | Source: chem-bla-ics
As a spoiler, the bottom line of my presentation is that we're not even using 10% of what the web technologies have to offer us. Slowly we are getting there, but too slow in my opinion. For some weird behavioral law, the larger the organization the less innovation gets done (some pointers).
Anyway, I only had 20 minutes, and in that time you cannot do justice to the web technologies.