-
Notifications
You must be signed in to change notification settings - Fork 0
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Meeting with supervisor (Dentica) #2
Comments
Dear @AChatzigoula, Kind regards, |
Hi Harry, Unfortunately we are not available Thursday and Friday. Would any time work for you tomorrow? |
3 similar comments
Hi Harry, Unfortunately we are not available Thursday and Friday. Would any time work for you tomorrow? |
Hi Harry, Unfortunately we are not available Thursday and Friday. Would any time work for you tomorrow? |
Hi Harry, Unfortunately we are not available Thursday and Friday. Would any time work for you tomorrow? |
Hi Zoe, The only slot that I can cancel tomorrow is 3-4:30pm (attending the VLDB 2020 Round table discussion on "Intelligent Data Exploration") but that's ok if it suits you as I want to know how things are going on and what help you require from OpenAIRE. Best, |
Hi Harry, No that's ok please dont cancel it. I will be traveling on Thursday but I guess I could participate in a call at 11am. Will you send us a zoom link? |
OK, great, I'll send a link for Thu 11am. |
Dentica Meeting - OpenAIRE-Advance Open Innovation Call Please join my meeting from your computer, tablet or smartphone. https://global.gotomeeting.com/join/830960165 You can also dial in using your phone. United States (Toll Free): 1 866 899 4679
United States: +1 (571) 317-3116
Access Code: 830-960-165 More phone numbers: Australia: +61 2 9091 7603
Austria: +43 7 2081 5337
Belgium: +32 28 93 7002
Canada: +1 (647) 497-9373
Denmark: +45 32 72 03 69
Finland: +358 923 17 0556
France: +33 187 210 241
Germany: +49 721 6059 6510
Ireland: +353 15 360 756
Italy: +39 0 230 57 81 80
Netherlands: +31 207 941 375
New Zealand: +64 9 913 2226
Norway: +47 21 93 37 37
Spain: +34 932 75 1230
Sweden: +46 853 527 818
Switzerland: +41 225 4599 60
United Kingdom: +44 20 3713 5011
New to GoToMeeting? Get the app now and be ready when your first meeting starts: https://global.gotomeeting.com/install/830960165 |
Dear Zoe, all, Regarding the issues you've been having with the OpenAIRE I've managed to get a reply from Claudio at CNR: |
So, he will get back to me with more details soon (he's on parental leave this week, but he might give me more info by tomorrow). |
Dear Harry, |
Dear Zoe, all, Claudio said that the new graph dump is represented according to the following json schema I'm still waiting for instructions on how you can access this dump on HDFS. |
Claudio now informed me that HDFS is not normally accessed by external users, so he's trying to get an answer from project admin if we can consider you as "extended tech team" and grant you access for the duration of phase 2, etc. |
Dear Harry, Thank you very much for your prompt actions. It would be great to have access to the file in this formal. Also, we'd certainly need to know if this is a format that you plan to stick to in order to adopt it. |
Dear Zoe, I just had an update from Claudio: " last week when we discussed the possibility to grant temporary access on HDFS to the OpenCall participants I didn’t keep in mind that the whole set of tools and web UIs we (tech team) use on a daily basis are reachable only through our VPN, so in my opinion this is a no-go for external users, I don’t think we can support them to configure the clients on their sides. So since Miriam won’t be back until next week we cannot expect the dump to be published on Zenodo until at least 10days/2weeks, therefore to cut the corner and save some time I’m trying to move the file containing the publications (plus the other result types) on some VM@CNR, where I’ll make it temporarily available for some time through an HTTP url. " I think that is the best and easiest solution for you at the moment. Let's wait for Claudio to copy the data to a site you can access and download it. Regarding the format, the official version will be published in about 10 days but it is very likely that it will be identical to this one. All the best, |
Actually he's just done it: _Harry the result.tar file is available from https://dev-openaire.d4science.org/dump/result.tar Regarding the data model, we’re going to use that JSON schema as reference model for these json dump files, but as I mentioned in skype with Thanasis &CO it still needs some adjustments before it can be officially published (edited)_ |
Hi Harry, thanks a lot! - I am forwarding this info to the team and we ;ll let you know if we have any questions!! |
Dear Harry, We have now downloaded and processed the json file. I would like to confirm that you would like us to provide our new dump to the OpenAire Research Graph in this format. Best |
Archive.zip result_sample.json contains five entries from your file ingredio_compounds_sample.json contains five entries from our data The final json file that we will deliver to you can be in the format of ingredio_compounds_sample.json or are there any other changes needed? Also, if you could send us the feedback we received form reviewers that would be great. |
Dear Zoe, So if I understand this correctly, in each line you provide a chemical compound (pubchem id) linked to a number of PMC publications, giving PMID, Pubchem_ID, Article (title), Journal, Abstract, and DOI for each. Are you going to be processing only PubMed articles or from other repostories too? I'll try to fetch the reviewers' comments from Phase 2 for you later today. |
The comment I got from CNR was: CNR is waiting also for the opinion of ICM who deals with mining representation in OpenAIRE. |
Sorry actually I truncated the full comment from Alessia at CNR, here it is: Alessia Bardi 4:01 PM (My comment... this is how we represent PDB entries in OpenAIRE, as external references, so Alessia is suggesting we do the same with chemicals). Alessia Bardi 4:12 PM |
Marek from ICM added that he is fine with the output provided and Alessia's comments but wanted to know if you are going to provide the dumps periodically to make them "consumable" by OpenAIRE or is your codebase planned to be run as a part of IIS (Information Inference Service of OpenAIRE)? As far as I remember from your proposal (paragraph on "Maintenance"), you will not be providing or integrating code with IIS but only providing updates. Am I correct? |
Here are the comments of the consensus report for Phase 2: Comments |
Dear Harry, Thank you for your feedback on all matters and for the proposal feedback! Here are some responses.
We can fill in the rest of the entries with no problems.
Best |
Dear Zoe, 1a) "qualifier" is meant to indicate the typology of the external reference. Currently the values supported by the relative vocabulary (dnet:externalReference_typologies) are the following:
So, depending on the type of the external reference you are going to provide us, you can pick one of those 4 values, or suggest new ones, so that we can extend our vocabulary definition. Here’s the json representation for two of them
1b) Regarding the field "query" at the moment it is not used. I suggest you keep it empty.
Best regards, |
Dear Harry, Thanks very much. We have an updated json file. Could you and your colleagues take a look so that we can finalize the format? Best |
Dear Harry, Zoe uploaded an older version of the sample. I am attaching the updated sample here. Best regards, |
Dear Gerasimos, thanks. |
Let me know if the above makes sense to you, else I'll give you Claudio's email to speak to him directly. |
Dear Harry, I tried to replicate Claudio's JSON structure, here is a sample. I also added the Journal's title at the very end of the JSON which was missing from Claudio's example. Best regards, |
Thanks, Gerasime, |
Dear Gerasime, Concerning the addition of Interestingly, we’re planning to rename that field as container to align with the Guidelines v4 but this will be done in the future. Otherwise, all else is fine. Best regards, |
Dear Harry, We are ready to submit D2) Project abstracts (summary of the actions to be completed during Phase 2) (dealine 15/9) D2.1) Documentation (deadline 28/9) Should we send to you or OpenAire directly? Also, you had mentioned that we may get a small extension for the end of the project (26/10/2020): Please do let us know if an extension will be granted, so that we plan accordingly. Best |
Dear Zoe, Please send it both to me and Coralia, because they have been very slow to reply lately, so I'd like to have a copy (they might send it to me very delayed). There has been complete silence from Coralia about the extension. Thanks for reminding me. I'll contact Nektaria there today to find out about it. Best regards, |
Great, thanks. Can you share your email here? Alternatively write me an email to zcournia at bioacademy.gr. |
Great, I've just sent you an email with my two email accounts (ΕΚΠΑ & ATHENA RC). |
Dear Zoe, I got a reply from Coralia saying that "the deliverables must be sent to [email protected] and we will make sure that all evaluators and respective supervisors receive them as well." In addition, this evening all SMEs will receive an email from Coralia with a slightly revised timeplan for the deadlines. Best regards, |
ΟΚ thanks - I will be sending the delis to this address with you on cc. |
Thanks, Zoe. |
Dear Harry, Regarding the journal tag change, could you please verify that this sample is in the correct format? Best regards, |
Dear Gerasimos, Sorry for the delayed reply, Claudio just replied that he tested the file "public_record.txt" and parsed it correctly as a Publication. So it all looks good. Best regards, |
That is great, thanks a lot for letting me know. Best regards, |
Dear Harry, We are all set for our conference call on October 26. Are there any guidelines/template that we should follow? Also, what is expected to present in the prototype demonstration ? Best |
Dear Zoe, I've sent a reply to the email thread with Nektaria. Best, |
Dear Harry, I have created a file that contains the publications which have been classified from a machine learning algorithm but I have a question regarding the structure of each entry. There are some entries that include Pubmed ID. For these entries I have added a second "qualifier" inside the "pid" tag. Should all entries have the second qualifier with empty value for those that do not contain Pubmed ID ? I will also attach a text file with two entries, one that does not contain Pubmed ID and one that does. Best regards, |
Dear Harry, I attach the sample file with the two entries here. Best regards, |
Dear Harry, Did you or Claudio had a chance to look at the file? Because we 'd like to present it on Monday. Otherwise, we ;ll present what we have and could can give us your feedback on Monday to work on the final version which will be delivered to you beginning of November. Best |
Dear Zoe and Gerasimos, my apologies for the delayed reply. I checked the JSON records in the publications_samples.txt file attached above and they are OK. The element Kind regards, |
Dear Zoe and Gerasimos, We are in the process of evaluation your phase 2 work and we would also like to receive a dump of the output you've produced. So far you have sent us a sample that we know can be ingested in OpenAIRE but the evaluation form requires us also to evaluate how the integration with OpenAIRE is also going on and how OpenAIRE benefits from your work. Many thanks, |
Of course, we have split it in 7 JSON files for convenience, and we can send you all of them. Best |
Dear Harry, We have created 7 JSON files, each one ~1.5GB. I can send them to you over email with wetransfer or another service or upload here a sample. Let me know. Best regards, |
Dear Gerasimos, For the evaluation (that we have to submit today) and just to tick the box that we have received the files, sending one of those today would suffice and we can discuss how to get access to the rest later. Many thanks, |
You may also use https://git-lfs.github.com |
Dear Harry, I have uploaded one of the files to Dropbox, this is the download link: https://www.dropbox.com/s/855pveyvavoooga/publications_export1.json?dl=0 Best regards, |
Thank you, Gerasime, |
Hi Harry, Was the file format ok? If there are any amendments we should do, please let us know. Best |
Dear Zoe, We had no time to ingest the data but a quick look I had tells me that all is fine. At this stage, that is all we needed in order to "tick the box" in the assessment form, so all is OK. So no amendments required now. We will share the assessment report when finalised, however, let me share with you two remarks that Corallia might contact you about, so that you can prepare a repose: ● From the estimation of costs on page 32 of D2.2, the price of a graphic designer is listed although the plan does not include any revision/creation of dedicated mock-ups and GUI for the prototype and final solution for the tender. Best regards, |
Dear Harry,
we received an email to contact you as our supervisor to discuss details about the implementation of OPENAIRE project Phase 2.
Can we arrange a meeting for tomorrow? We are available at 10am or 1pm EEST.
Best,
Ingredio team
The text was updated successfully, but these errors were encountered: