Open mattodd opened 3 years ago
cdsouthan
commented
3 years ago Suggest to add rule "Donating parties are strongly encouraged to a) check if the compound already has a PubChem Compound ID (CID) or b) arrange to submit any structures so they then get a CID
mattodd
commented
3 years ago Hi @cdsouthan - thanks for this. Certainly valuable, but I think the project itself could/would deal with this. I want to keep the requirements on potential contributors as light as possible, to encourage the contributions.
miquelduranfrigola
commented
3 years ago Good initiative. Are you planning to do any initial checks (HPC, mass spectrometry) to the submitted molecules?
Open drug discovery projects have several advantages, and one of those needs to be the ease with which people can contribute physical samples for evaluation: either molecules they have made for the project specifically, or molecules that may be useful and are just sitting in a freezer.
People have donated molecules to open projects before in various ways, for example synthesizing them in their own labs and having them tested nearby (e.g., Patrick Thomson and Chase Smith over in OSM OpenSourceMalaria/OSM_To_Do_List#487), or digging them out of the freezer and sending them in (e.g., Helen Hailes for OSM Series 5, and DNDi (opensourceantibiotics/Series-2-Diarylimidazoles#27) and Lori Ferrins (opensourceantibiotics/Series-2-Diarylimidazoles#48) in OSA Series 2). Lots of researchers are interested in seeing whether their fridge contains something useful for drug discovery, serendipitously or because of perceived molecular similarity. But I think lots of those people worry about getting bogged down in legal paperwork, and some industry folks are maybe worried that if they donate molecules they are somehow obligated to do more.
We've never had any clear arrangements for these sample donations, but as we move to scale up more open projects, clarity is needed. The general guidelines for open projects are as described in the Six Laws, and the overall license is always CC-BY-4.0 (the Wikipedia licence) but these don't adequately cover physical samples, so we need something fresh. We'd like to avoid, if possible, the need for MTAs (even openMTA, though I'm open to be persuaded just to adopt this) just because that slows things down and increases transactional costs dramatically. There are some good rules available for requesting compounds that have been devised by the SGC (Paper), i.e. where someone wants to receive a chemical probe from the SGC (the reverse of what we're talking about here). The nice thing about the SGC terms is that the user has to agree to the rules as part of the request. Similarly for open drug discovery projects: the rules need to be agreed to as part of the submission.
We got chatting about this in a recent Open Source Antibiotics meeting opensourceantibiotics/Series-2-Diarylimidazoles#45 and have consulted on the guidelines.
The most recent version is here.
The guidelines cover things like the obligations on the contributor and the open project, potential future uses of the samples, and what happens if future data are derived.
These rules will be updated onto the current molecule submission page for OSA, and they can be cloned for other open projects.
I'd love to hear any suggestions (particularly from potential industry contributors) please comment below or tweet us at or get in touch with me by email or on LinkedIn.
Do these rules work, and is there anything that's missing?
(there are lots of ways in which we might improve the process of connecting molecules with the people who might need them, ranging from use of commercial vendors through to Molecular Craigslist type sites that I've been talking about forever through to newer things I and others are thinking about, but whatever we do we'll need simple submission guidelines, and terms).