From alex.mozejko at databiology.com Thu Jul 2 03:07:33 2020 From: alex.mozejko at databiology.com (Alex Mozejko) Date: Thu, 2 Jul 2020 10:07:33 +0000 Subject: [bioontology-support] Databiology: Default web portal credentials Message-ID: Hello, We have recently deployed the Bioportal appliance to one of our AWS environments but can?t seem to login using the credentials: Username: admin Password: changemeNOW Whenever I try I get the error: ?Errors On Form. Invalid account name/password combination? The default ssh user credentials worked and I can confirm ssh access. I can also confirm that creating a new user and uploading an ontology works, so good news there ? The process I followed to deploy this appliance is as follows: 1. Download OVA image from https://bioportal.bioontology.org/virtual_appliance 2. Copy OVA to s3 bucket 3. Use aws cli to convert image to AMI as detailed here 4. Launched virtual machine using the converted AMI 5. Navigate to portal 6. Try to login as admin 7. Get error Can you please confirm that the credentials I?m trying to use are correct? And is there a way to reset the ?admin? user?s password? Thanks, Alex. -------------- next part -------------- An HTML attachment was scrubbed... URL: From alex.skrenchuk at stanford.edu Thu Jul 2 14:42:28 2020 From: alex.skrenchuk at stanford.edu (Alex Skrenchuk) Date: Thu, 2 Jul 2020 21:42:28 +0000 Subject: [bioontology-support] Databiology: Default web portal credentials Message-ID: HI Alex, We have not yet experimented with importing OVA to AWS because we are counting that the majority of users will deploy OntoPortal from the AWS marketplace. We were recently been made aware that version 3.0.1 of the appliance sometimes doesn?t initialize properly in AWS during the first boot which could be usually resolved with a second reboot. During the very first boot of the appliance we have a firstboot script that resets API keys for the Web UI and Admin user. If it detects that appliance is running in AWS then it will also resets Admin password to match the instance-id of your EC2 instance. First I would try to use the EC2 instance-id for admin password and if that doesn?t work then you could try to force re-run of the firstboot script. ssh to instance as centos user and: sudo touch /srv/ontoportal/firstboot sudo chown ontoportal /srv/ontoportal/firstboot sudo reboot -Alex From: bioontology-support on behalf of Alex Mozejko Date: Thursday, July 2, 2020 at 8:00 AM To: "support at bioontology.org" Subject: [bioontology-support] Databiology: Default web portal credentials Hello, We have recently deployed the Bioportal appliance to one of our AWS environments but can?t seem to login using the credentials: Username: admin Password: changemeNOW Whenever I try I get the error: ?Errors On Form. Invalid account name/password combination? The default ssh user credentials worked and I can confirm ssh access. I can also confirm that creating a new user and uploading an ontology works, so good news there ? The process I followed to deploy this appliance is as follows: 1. Download OVA image from https://bioportal.bioontology.org/virtual_appliance 2. Copy OVA to s3 bucket 3. Use aws cli to convert image to AMI as detailed here 4. Launched virtual machine using the converted AMI 5. Navigate to portal 6. Try to login as admin 7. Get error Can you please confirm that the credentials I?m trying to use are correct? And is there a way to reset the ?admin? user?s password? Thanks, Alex. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonquet at lirmm.fr Mon Jul 6 02:16:35 2020 From: jonquet at lirmm.fr (Clement Jonquet) Date: Mon, 6 Jul 2020 11:16:35 +0200 Subject: [bioontology-support] Remove MEDRA Message-ID: <7BB1BD09-1F3B-4225-993E-7DDDF8C34FB3@lirmm.fr> This ontology is empty and create confusion with the real Meddra: http://bioportal.bioontology.org/ontologies/MEDRA/?p=summary I would suggest to remove it from BioPortal. Bye Clement -------------- next part -------------- An HTML attachment was scrubbed... URL: From vk396 at njit.edu Mon Jul 6 11:45:23 2020 From: vk396 at njit.edu (Kuttichi Keloth, Vipina) Date: Mon, 6 Jul 2020 14:45:23 -0400 Subject: [bioontology-support] Processing two ontologies Message-ID: Hi, Could you please process two ontologies (CIDIO_AUX and ACT_COVID) uploaded on BioPortal? It was uploaded on July 1st. Thank you. Vipina -------------- next part -------------- An HTML attachment was scrubbed... URL: From vk396 at njit.edu Mon Jul 6 14:26:24 2020 From: vk396 at njit.edu (Kuttichi Keloth, Vipina) Date: Mon, 6 Jul 2020 17:26:24 -0400 Subject: [bioontology-support] Processing two ontologies In-Reply-To: References: Message-ID: The ACT_COVID has been processed. But CIDIO_AUX is not giving any annotations when using the Annotator to annotate text. Could you please look into this? Thank you. Vipina On Mon, Jul 6, 2020 at 2:45 PM Kuttichi Keloth, Vipina wrote: > Hi, > > Could you please process two ontologies (CIDIO_AUX and ACT_COVID) > uploaded on BioPortal? > It was uploaded on July 1st. > > Thank you. > Vipina > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Mon Jul 6 14:39:45 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Mon, 6 Jul 2020 21:39:45 +0000 Subject: [bioontology-support] Processing two ontologies In-Reply-To: References: Message-ID: Hi Vipina, I am working on reprocessing both ontologies. I?ll keep you posted once the process completes. Thank you for your patience. Michael On Jul 6, 2020, at 2:26 PM, Kuttichi Keloth, Vipina > wrote: The ACT_COVID has been processed. But CIDIO_AUX is not giving any annotations when using the Annotator to annotate text. Could you please look into this? Thank you. Vipina On Mon, Jul 6, 2020 at 2:45 PM Kuttichi Keloth, Vipina > wrote: Hi, Could you please process two ontologies (CIDIO_AUX and ACT_COVID) uploaded on BioPortal? It was uploaded on July 1st. Thank you. Vipina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vk396 at njit.edu Mon Jul 6 14:40:35 2020 From: vk396 at njit.edu (Kuttichi Keloth, Vipina) Date: Mon, 6 Jul 2020 17:40:35 -0400 Subject: [bioontology-support] Processing two ontologies In-Reply-To: References: Message-ID: Ok. Thank you so much. Vipina On Mon, Jul 6, 2020 at 5:39 PM Michael Dorf wrote: > Hi Vipina, > > I am working on reprocessing both ontologies. I?ll keep you posted once > the process completes. > > Thank you for your patience. > > Michael > > > On Jul 6, 2020, at 2:26 PM, Kuttichi Keloth, Vipina > wrote: > > The ACT_COVID has been processed. > > But CIDIO_AUX is not giving any annotations when using the Annotator to > annotate text. > Could you please look into this? > > Thank you. > Vipina > > On Mon, Jul 6, 2020 at 2:45 PM Kuttichi Keloth, Vipina > wrote: > >> Hi, >> >> Could you please process two ontologies (CIDIO_AUX and ACT_COVID) >> uploaded on BioPortal? >> It was uploaded on July 1st. >> >> Thank you. >> Vipina >> > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Mon Jul 6 16:07:31 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Mon, 6 Jul 2020 23:07:31 +0000 Subject: [bioontology-support] Processing two ontologies In-Reply-To: References: Message-ID: <10B9CF24-4620-4BDA-8323-095DB179C88B@stanford.edu> Hi Vipina, Both of your ontologies have finished processing. Let me know if you are still seeing any issues. Thank you! Michael On Jul 6, 2020, at 2:40 PM, Kuttichi Keloth, Vipina > wrote: Ok. Thank you so much. Vipina On Mon, Jul 6, 2020 at 5:39 PM Michael Dorf > wrote: Hi Vipina, I am working on reprocessing both ontologies. I?ll keep you posted once the process completes. Thank you for your patience. Michael On Jul 6, 2020, at 2:26 PM, Kuttichi Keloth, Vipina > wrote: The ACT_COVID has been processed. But CIDIO_AUX is not giving any annotations when using the Annotator to annotate text. Could you please look into this? Thank you. Vipina On Mon, Jul 6, 2020 at 2:45 PM Kuttichi Keloth, Vipina > wrote: Hi, Could you please process two ontologies (CIDIO_AUX and ACT_COVID) uploaded on BioPortal? It was uploaded on July 1st. Thank you. Vipina _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vk396 at njit.edu Mon Jul 6 16:14:22 2020 From: vk396 at njit.edu (Kuttichi Keloth, Vipina) Date: Mon, 6 Jul 2020 19:14:22 -0400 Subject: [bioontology-support] Processing two ontologies In-Reply-To: <10B9CF24-4620-4BDA-8323-095DB179C88B@stanford.edu> References: <10B9CF24-4620-4BDA-8323-095DB179C88B@stanford.edu> Message-ID: Thanks a lot. Vipina On Mon, Jul 6, 2020 at 7:07 PM Michael Dorf wrote: > Hi Vipina, > > Both of your ontologies have finished processing. Let me know if you are > still seeing any issues. > > Thank you! > > Michael > > On Jul 6, 2020, at 2:40 PM, Kuttichi Keloth, Vipina > wrote: > > Ok. Thank you so much. > > Vipina > > On Mon, Jul 6, 2020 at 5:39 PM Michael Dorf wrote: > >> Hi Vipina, >> >> I am working on reprocessing both ontologies. I?ll keep you posted once >> the process completes. >> >> Thank you for your patience. >> >> Michael >> >> >> On Jul 6, 2020, at 2:26 PM, Kuttichi Keloth, Vipina >> wrote: >> >> The ACT_COVID has been processed. >> >> But CIDIO_AUX is not giving any annotations when using the Annotator to >> annotate text. >> Could you please look into this? >> >> Thank you. >> Vipina >> >> On Mon, Jul 6, 2020 at 2:45 PM Kuttichi Keloth, Vipina >> wrote: >> >>> Hi, >>> >>> Could you please process two ontologies (CIDIO_AUX and ACT_COVID) >>> uploaded on BioPortal? >>> It was uploaded on July 1st. >>> >>> Thank you. >>> Vipina >>> >> _______________________________________________ >> bioontology-support mailing list >> bioontology-support at lists.stanford.edu >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From soldatova.larisa at gmail.com Tue Jul 7 06:02:16 2020 From: soldatova.larisa at gmail.com (Larisa Soldatova) Date: Tue, 7 Jul 2020 14:02:16 +0100 Subject: [bioontology-support] please remove me from this list Message-ID: Hi, I must have gotten on this list by mistake. Please can you remove me so I do not receive copies of all your emails? Thanks, Larisa -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue Jul 7 14:41:49 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 7 Jul 2020 21:41:49 +0000 Subject: [bioontology-support] please remove me from this list In-Reply-To: References: Message-ID: <99E16791-338F-472B-BEC9-406C48ADEF82@stanford.edu> Hi Larisa, You should receive an email with further instructions on how to unsubscribe from our list. Let us know if you haven?t received one. Thanks, Michael > On Jul 7, 2020, at 6:02 AM, Larisa Soldatova wrote: > > Hi, > > I must have gotten on this list by mistake. Please can you remove me so I do not receive copies of all your emails? > > Thanks, > Larisa > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support From support at bioontology.org Mon Jul 13 00:21:34 2020 From: support at bioontology.org (support at bioontology.org) Date: Mon, 13 Jul 2020 00:21:34 -0700 Subject: [bioontology-support] [BioPortal] Feedback from ALQAHATANI SAEED FARES Message-ID: <5f0c0b7e49be6_60a220ebeb896432@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Mon Jul 13 07:33:08 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Mon, 13 Jul 2020 14:33:08 +0000 Subject: [bioontology-support] [BioPortal] Feedback from ALQAHATANI SAEED FARES In-Reply-To: <5f0c0b7e49be6_60a220ebeb896432@ncbo-prd-app-09.stanford.edu.mail> References: <5f0c0b7e49be6_60a220ebeb896432@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <1F07E0C8-8849-4EED-8DE6-88ACD5D84BEA@stanford.edu> Hello Saeed, Thanks for your request. I can only offer you the permissions already granted by our terms of use, which can be found at https://ncbo.bioontology.org/terms. Hopefully that is sufficient for your needs. John On Jul 13, 2020, at 12:21 AM, support at bioontology.org wrote: Name: ALQAHATANI SAEED FARES Email: dr-s2001 at hotmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FTRAK Feedback: I have a research proposal entitled "Digital intervention development to promote self-management and diagnosis of the knee", so I need to take your permission to take some information from this application. Thank you for your cooperation kind regards, Saeed _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Junaid_Bhatti at manulife.com Tue Jul 14 08:48:16 2020 From: Junaid_Bhatti at manulife.com (Junaid Bhatti) Date: Tue, 14 Jul 2020 15:48:16 +0000 Subject: [bioontology-support] Queries on REST API call limit and licensing Message-ID: <8FB65458-D0DD-4D04-9157-D193405DFDDB@mfcgd.com> Greetings: I am a Senior Data Scientist at an life insurance company in North America. I have reviewed the website (https://bioportal.bioontology.org/) and it is unclear to me whether there is a limit in usage if you are part of a private company. Specifically, is there a limit on REST API calls? Secondly, is there a requirement to obtain any license or permission restrictions in the use of NCBO portal by private companies? Thanking you in anticipation for your responses to my queries. Best regards, Junaid Junaid A. Bhatti, PhD, MSc, MBBS. Sr. Data Scientist | Underwriting COE | Advanced Analytics Manulife E junaid_bhatti at manulife.com T 416 687 3148 (Direct) Internal ext. 273148 M 647 237 6284 250 Bloor St. East, Toronto, ON, M4W 1E5 [cid:image002.png at 01D492D2.F591D670] STATEMENT OF CONFIDENTIALITY The information contained in this email message and any attachments may be confidential and legally privileged and is intended for the use of the addressee(s) only. If you are not an intended recipient, please: (1) notify me immediately by replying to this message; (2) do not use, disseminate, distribute or reproduce any part of the message or any attachment; and (3) destroy all copies of this message and any attachments. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 3895 bytes Desc: image001.png URL: From jgraybeal at stanford.edu Wed Jul 15 18:53:38 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 16 Jul 2020 01:53:38 +0000 Subject: [bioontology-support] Queries on REST API call limit and licensing In-Reply-To: <8FB65458-D0DD-4D04-9157-D193405DFDDB@mfcgd.com> References: <8FB65458-D0DD-4D04-9157-D193405DFDDB@mfcgd.com> Message-ID: <889A5211-CE46-4349-9F7F-4915615C1B89@stanford.edu> Hello Junaid, thank you for your questions. There is only one enforced limit on access to BioPortal right now, and that is that API requests are limited to 15 per second (rarely reduced to 5 per second in we have too heavy a load. When this happens you would get an error message as your reply message. There are practical limits that are enforced if certain calls are overused. Any Recommender query that is long will heavily load the system, as will requests for all terms and their properties from very large ontologies (even though this request is paged). There are some other requests that might be problematic?if you have questions about specific queries you can email them to the support list. Too many heavily loaded queries in a row will cause the system to become non-responsive, and sometimes to fail, forcing us to restart it. If we find a single entity is making so many calls that causes problems for the system, we will attempt to contact that user to request a modification. If we can not reach the user, or if we determine the user is not complying with our terms, we will blacklist the user's API key, or their IP address if they are querying anonymously. There are permission restrictions on certain BioPortal ontologies, and as our Terms (https://ncbo.bioontology.org/terms) indicate, it is up to the users of BioPortal to ensure they are following the license requirements of each ontology contained in BioPortal. (These license requirements are specified in the summary metadata, displayed on the summary page of each ontology.) We do not restrict usage of BioPortal by private companies. However, we find that many companies?typically ones that ask about usage limits :-) ?need to use BioPortal more heavily than the above constraints allow. Also private companies often don't want to risk their queries becoming known publicly. For that reason, we make available the OntoPortal (https://ontoportal.org/the-ontoportal-virtual-appliance/), which private companies can install locally and populate with whatever ontologies they want to use. (Alternatively, they can make arrangements with our team to provide this service, assuming available resources on our side.) The instructions for obtaining and installing OntoPortal are at https://ontoportal.github.io/administration, and a registration is required. Registration terms for commercial companies may require discussion with the OntoPortal providers (see the documentation). I hope this helps with your questions. You can reply with questions to the support list, or contact me directly (jgraybeal at stanford.edu) if you want further information about registration costs for OntoPortal. John On Jul 14, 2020, at 8:48 AM, Junaid Bhatti > wrote: Greetings: I am a Senior Data Scientist at an life insurance company in North America. I have reviewed the website (https://bioportal.bioontology.org/) and it is unclear to me whether there is a limit in usage if you are part of a private company. Specifically, is there a limit on REST API calls? Secondly, is there a requirement to obtain any license or permission restrictions in the use of NCBO portal by private companies? Thanking you in anticipation for your responses to my queries. Best regards, Junaid Junaid A. Bhatti, PhD, MSc, MBBS. Sr. Data Scientist | Underwriting COE | Advanced Analytics Manulife ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From support at bioontology.org Wed Jul 15 10:57:55 2020 From: support at bioontology.org (support at bioontology.org) Date: Wed, 15 Jul 2020 10:57:55 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Emma Vos Message-ID: <5f0f43a380552_8cf27449f480627@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From brodriguez at integraltx.com Thu Jul 16 07:09:00 2020 From: brodriguez at integraltx.com (Benjamin Rodriguez) Date: Thu, 16 Jul 2020 10:09:00 -0400 Subject: [bioontology-support] Account details error, seeking API key Message-ID: Dear Support, I registered for an account under brodriguez. I need to obtain an API key. I am able to log in, but I receive a "something has gone wrong" error message when I click link for account details. I assume the API key is under account details. Can you give me my API key? Thanks, Ben Disclaimer The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you should delete this message. You are hereby notified that any disclosure, copying, distribution or taking action in relation to the contents of this information is strictly prohibited and may be unlawful. -------------- next part -------------- An HTML attachment was scrubbed... URL: From brayanrodbajo at gmail.com Thu Jul 16 04:48:48 2020 From: brayanrodbajo at gmail.com (Brayan Rodriguez) Date: Thu, 16 Jul 2020 06:48:48 -0500 Subject: [bioontology-support] Get altLabel and label Message-ID: Hi. I am writing due to the need for extracting the properties label and altLabel of a specific term through the API (data.bioontology.org). Do you know how can I get this information? Thank you in advance. Best, -- Brayan Rodr?guez. Systems Engineer, Universidad del Valle. Master of Computer Engineering, Universidad Icesi. Cali, Colombia. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Thu Jul 16 10:58:35 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 16 Jul 2020 17:58:35 +0000 Subject: [bioontology-support] Get altLabel and label In-Reply-To: References: Message-ID: <85BDBAD1-15A7-429E-A136-CF6D8FC821A5@stanford.edu> Hi Brayan, Thank you for your question. Depending on the ontology you are working with, the fields ?label? and ?altLabel? may or may not exist. Your best solution for extracting these fields is by asking for ALL of the properties of a given class using the ?display=properties? query parameter: http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F122040007?include=prefLabel,synonym,definition,cui,semanticType,obsolete,properties http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C34952?include=prefLabel,synonym,definition,cui,semanticType,obsolete,properties If you know the property name that contains the data you need (the names/namespaces can be different for different ontologies), you can extract them from the ?properties? collection. Let me know if this works for you. Michael On Jul 16, 2020, at 4:48 AM, Brayan Rodriguez > wrote: Hi. I am writing due to the need for extracting the properties label and altLabel of a specific term through the API (data.bioontology.org). Do you know how can I get this information? Thank you in advance. Best, -- Brayan Rodr?guez. Systems Engineer, Universidad del Valle. Master of Computer Engineering, Universidad Icesi. Cali, Colombia. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vk396 at njit.edu Thu Jul 16 11:45:51 2020 From: vk396 at njit.edu (Kuttichi Keloth, Vipina) Date: Thu, 16 Jul 2020 14:45:51 -0400 Subject: [bioontology-support] BioPortal not allowing uploads Message-ID: Hi, I guess you are notified about the issue. The submit ontology page returns an error. Could you please look into this? Thank you. Vipina -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Thu Jul 16 14:25:12 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 16 Jul 2020 21:25:12 +0000 Subject: [bioontology-support] BioPortal not allowing uploads In-Reply-To: References: Message-ID: Hi Vipina, Thank you for your report. Apologies for that. There was a system glitch that required clearing of our internal cache repositories. The ontology submission page is now back to operational. Let us know if you are still experiencing issues. Thank you! Michael > On Jul 16, 2020, at 11:45 AM, Kuttichi Keloth, Vipina wrote: > > Hi, > > I guess you are notified about the issue. The submit ontology page returns an error. > > Could you please look into this? > > Thank you. > Vipina > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support From mdorf at stanford.edu Thu Jul 16 14:28:47 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 16 Jul 2020 21:28:47 +0000 Subject: [bioontology-support] Account details error, seeking API key In-Reply-To: References: Message-ID: <7C8C0DF2-4D13-4478-9469-683B1AA79CA8@stanford.edu> Hi Benjamin, Thank you for your report. Please accept my apologies for the downtime. The problem was caused by a system glitch that required clearing of our internal cache repositories. The account details page is now back to operational, and you should be able to retrieve your API key directly from there. Let us know if you are still experiencing issues. Thank you! Michael On Jul 16, 2020, at 7:09 AM, Benjamin Rodriguez > wrote: Dear Support, I registered for an account under brodriguez. I need to obtain an API key. I am able to log in, but I receive a "something has gone wrong" error message when I click link for account details. I assume the API key is under account details. Can you give me my API key? Thanks, Ben Disclaimer The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you should delete this message. You are hereby notified that any disclosure, copying, distribution or taking action in relation to the contents of this information is strictly prohibited and may be unlawful. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vk396 at njit.edu Thu Jul 16 14:29:43 2020 From: vk396 at njit.edu (Kuttichi Keloth, Vipina) Date: Thu, 16 Jul 2020 17:29:43 -0400 Subject: [bioontology-support] BioPortal not allowing uploads In-Reply-To: References: Message-ID: Thank you. I was able to upload some time back ( CIDIT_V1_2). But I guess there is a processing error. It shows under the submissions - uploaded,* Error rdf.* *Could you please reprocess it?* *Thank you.* *Vipina* On Thu, Jul 16, 2020 at 5:25 PM Michael Dorf wrote: > Hi Vipina, > > Thank you for your report. Apologies for that. There was a system glitch > that required clearing of our internal cache repositories. The ontology > submission page is now back to operational. Let us know if you are still > experiencing issues. > > Thank you! > > Michael > > > On Jul 16, 2020, at 11:45 AM, Kuttichi Keloth, Vipina > wrote: > > > > Hi, > > > > I guess you are notified about the issue. The submit ontology page > returns an error. > > > > Could you please look into this? > > > > Thank you. > > Vipina > > _______________________________________________ > > bioontology-support mailing list > > bioontology-support at lists.stanford.edu > > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Thu Jul 16 14:35:49 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Thu, 16 Jul 2020 21:35:49 +0000 Subject: [bioontology-support] BioPortal not allowing uploads In-Reply-To: References: Message-ID: Hi Vipina, I am seeing parsing errors during the processing of your ontology, which I need some time to investigate. I?ll keep you posted on my findings. Thanks, Michael On Jul 16, 2020, at 2:29 PM, Kuttichi Keloth, Vipina > wrote: Thank you. I was able to upload some time back ( CIDIT_V1_2). But I guess there is a processing error. It shows under the submissions - uploaded, Error rdf. Could you please reprocess it? Thank you. Vipina On Thu, Jul 16, 2020 at 5:25 PM Michael Dorf > wrote: Hi Vipina, Thank you for your report. Apologies for that. There was a system glitch that required clearing of our internal cache repositories. The ontology submission page is now back to operational. Let us know if you are still experiencing issues. Thank you! Michael > On Jul 16, 2020, at 11:45 AM, Kuttichi Keloth, Vipina > wrote: > > Hi, > > I guess you are notified about the issue. The submit ontology page returns an error. > > Could you please look into this? > > Thank you. > Vipina > _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Thu Jul 16 14:39:53 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Thu, 16 Jul 2020 21:39:53 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Emma Vos In-Reply-To: <5f0f43a380552_8cf27449f480627@ncbo-prd-app-09.stanford.edu.mail> References: <5f0f43a380552_8cf27449f480627@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hello Emma, On Jul 15, 2020, at 10:57 AM, support at bioontology.org wrote: I wanted to annotate some cell types (e.g. "monocyte") with Cell Ontology terms, using the Annotator tool. Unfortunately, this didn't work. When browsing through the Cell Ontology, I saw that part of the ontology is missing in BioPortal. For example, Cell Ontology contains a term for "monocyte": http://purl.obolibrary.org/obo/CL_0000576 . But this term is not included in the Cell Ontology on BioPortal. Hence why I couldn't annotate this "monocyte" properly using the Annotator tool. Another issue I had was with downloading the CSV file of Cell Ontology. I get the following error: "Cannot read latest submission upload file: /srv/ncbo/repository/CL/73/CL.csv.gz" Apologies for the inconvenience. It appears there was an error that occurred during the processing of the latest submission of the Cell Ontology. I reprocessed the ontology and the issues you reported are resolved - the CSV file is downloadable again, and the classes page appears normal. Kind regards, Jennifer [cid:5B3100B2-FB05-4940-8D61-C4EC0351EE9E at stanford.edu] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2020-07-16 14.36.38.png Type: image/png Size: 289481 bytes Desc: Screenshot 2020-07-16 14.36.38.png URL: From vendetti at stanford.edu Thu Jul 16 20:57:01 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 17 Jul 2020 03:57:01 +0000 Subject: [bioontology-support] BioPortal not allowing uploads In-Reply-To: References: Message-ID: <1778A813-CE93-4DB0-8AEE-B67BF3115E82@stanford.edu> Hello Vipina, There are 2,535 occurrences in your ontology source file where the value of rdf:about has a leading space character. One such example can be seen on line 156,587: > > The ontology parsing library we use internally considers these leading > space characters illegal: > > > Detailed logs: > > -------------------------------------------------------------------------------- > Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser at 985696 > Stack trace: > org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException: > [line=156589:column=79] IRI ' > http://purl.obolibrary.org/obo/CIDO_UMLS_C5203670' cannot be resolved > against current base IRI http://purl.obolibrary.org/obo/cido.owl reason > is: Illegal character in scheme name at index 0: %20http:// > purl.obolibrary.org/obo/CIDO_UMLS_C5203670 > org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:76) > > uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:221) > > > I ran a search and replace over the file to remove these leading space > characters and uploaded the modified version of your ontology as a new > submission. It?s fully processed and available in BioPortal now. If you > want to submit updates, you?ll need to correct these leading space > characters in your original source file. > > Kind regards, > Jennifer > > > > On Jul 16, 2020, at 2:29 PM, Kuttichi Keloth, Vipina > wrote: > > Thank you. I was able to upload some time back ( CIDIT_V1_2). But I guess > there is a processing error. > It shows under the submissions - uploaded,* Error rdf.* > > *Could you please reprocess it?* > > *Thank you.* > *Vipina* > > On Thu, Jul 16, 2020 at 5:25 PM Michael Dorf wrote: > >> Hi Vipina, >> >> Thank you for your report. Apologies for that. There was a system glitch >> that required clearing of our internal cache repositories. The ontology >> submission page is now back to operational. Let us know if you are still >> experiencing issues. >> >> Thank you! >> >> Michael >> >> > On Jul 16, 2020, at 11:45 AM, Kuttichi Keloth, Vipina >> wrote: >> > >> > Hi, >> > >> > I guess you are notified about the issue. The submit ontology page >> returns an error. >> > >> > Could you please look into this? >> > >> > Thank you. >> > Vipina >> > _______________________________________________ >> > bioontology-support mailing list >> > bioontology-support at lists.stanford.edu >> > https://mailman.stanford.edu/mailman/listinfo/bioontology-support >> >> _______________________________________________ > bioontology-support mailing list > bioontology-support at lists.stanford.edu > https://mailman.stanford.edu/mailman/listinfo/bioontology-support > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From soldatova.larisa at gmail.com Mon Jul 20 07:29:16 2020 From: soldatova.larisa at gmail.com (Larisa Soldatova) Date: Mon, 20 Jul 2020 15:29:16 +0100 Subject: [bioontology-support] problems with submitting a new ontology Message-ID: Dear Support Team, I am trying to submit an ontology - TML, and I am getting error messages after filling in metadata for this ontology. So I am unable to actually submit a file. Today I tried to do this again, and I got a message that 'TML' is already taken. I assume that metadata actually were created, but it did not go any further. Please can you check what is wrong? I need to submit this ontology, it is important for our publication. Thank you, Larisa -------------- next part -------------- An HTML attachment was scrubbed... URL: From vendetti at stanford.edu Mon Jul 20 10:17:56 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Mon, 20 Jul 2020 17:17:56 +0000 Subject: [bioontology-support] problems with submitting a new ontology In-Reply-To: References: Message-ID: <3EEEF389-CC9E-4633-9E55-AFBA610DE48C@stanford.edu> Hello Larisa, On Jul 20, 2020, at 7:29 AM, Larisa Soldatova > wrote: I am trying to submit an ontology - TML, and I am getting error messages after filling in metadata for this ontology. So I am unable to actually submit a file. Today I tried to do this again, and I got a message that 'TML' is already taken. I assume that metadata actually were created, but it did not go any further. Apologies for the inconvenience. We?re aware of this problem and are currently troubleshooting. In the mean time, you should be able to submit an ontology file by navigating to your ontology entry page: http://bioportal.bioontology.org/ontologies/TML ? and clicking the ?Add submission? button at the top of the Submissions table. I had to flush our application caches to make your ontology entry visible. You may need to refresh your browser page / cache to see the entry now. Kind regards, Jennifer [cid:A0B94090-97C4-4B5C-9A4D-50A52E84D7F4 at lan] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2020-07-20 10.15.14.png Type: image/png Size: 104524 bytes Desc: Screenshot 2020-07-20 10.15.14.png URL: From support at bioontology.org Tue Jul 21 11:34:20 2020 From: support at bioontology.org (support at bioontology.org) Date: Tue, 21 Jul 2020 11:34:20 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Melissa Locke Message-ID: <5f17352c48da4_725226cd174753b4@ncbo-prd-app-08.stanford.edu.mail> An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Tue Jul 21 13:40:50 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Tue, 21 Jul 2020 20:40:50 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Melissa Locke In-Reply-To: <5f17352c48da4_725226cd174753b4@ncbo-prd-app-08.stanford.edu.mail> References: <5f17352c48da4_725226cd174753b4@ncbo-prd-app-08.stanford.edu.mail> Message-ID: <9D82FE6D-466C-4426-885E-3EF51268AB08@stanford.edu> Hi Melissa, For online use, I'd suggest you link to the web site (https://bioontology.org) and/or the application (https://bioportal.bioontology.org). However, we sadly note that the CPT term descriptions are going to go away soon. At the request of the ontology providers, we are going to be removing the ontology contents from BioPortal with our next UMLS release, which will happen in a few weeks. There will still be a summary page, but the ontology terms will no longer be on the site. John On Jul 21, 2020, at 11:34 AM, support at bioontology.org wrote: Name: Melissa Locke Email: mlocke at cleverleyassociates.com Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3D0001U Feedback: Hi! We would like to use the BioPortal CPT descriptions to help our clients comply with new CMS disclosure guidelines. We saw your "how to cite" page, but wanted to verify that this is the preferred way for citing your site on a website (not a research paper). Is the "how to cite" the preferred online citation? Thanks! _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From alex.mozejko at databiology.com Wed Jul 22 23:02:15 2020 From: alex.mozejko at databiology.com (Alex Mozejko) Date: Thu, 23 Jul 2020 06:02:15 +0000 Subject: [bioontology-support] Databiology: Default web portal credentials In-Reply-To: References: Message-ID: Hi Alex, Apologies for taking so long to get back to you on this. Thank you very much to the ?firstboot? tip, that worked a treat. A couple of weeks ago I created a request at https://license.ontoportal.org/licenses for appliance id d8d04b7b-577b-4d09-b40a-82ccc0a12b99. Can you please double check that this hasn?t been lost? I?m happy to provide additional information if required. Also we?re having issues loading new Ontologies, we can use the portal to upload a file and it appears in the list however when clicking into the Ontology, the summary tab shows: Metrics We have not yet calculated metrics for ONTOLOGY Visits We are still collecting data for ONTOLOGY And the ?classes? tab reports: ?Problem retrieving classes? Does any of this sound familiar? Or can you suggest some logs to read which might point us in a right direction to solve? Apologies again for taking so long to respond. Thanks, Alex. From: Alex Skrenchuk Sent: Friday, 3 July 2020 5:42 AM To: Alex Mozejko ; support at bioontology.org Subject: Re: [bioontology-support] Databiology: Default web portal credentials HI Alex, We have not yet experimented with importing OVA to AWS because we are counting that the majority of users will deploy OntoPortal from the AWS marketplace. We were recently been made aware that version 3.0.1 of the appliance sometimes doesn?t initialize properly in AWS during the first boot which could be usually resolved with a second reboot. During the very first boot of the appliance we have a firstboot script that resets API keys for the Web UI and Admin user. If it detects that appliance is running in AWS then it will also resets Admin password to match the instance-id of your EC2 instance. First I would try to use the EC2 instance-id for admin password and if that doesn?t work then you could try to force re-run of the firstboot script. ssh to instance as centos user and: sudo touch /srv/ontoportal/firstboot sudo chown ontoportal /srv/ontoportal/firstboot sudo reboot -Alex From: bioontology-support > on behalf of Alex Mozejko > Date: Thursday, July 2, 2020 at 8:00 AM To: "support at bioontology.org" > Subject: [bioontology-support] Databiology: Default web portal credentials Hello, We have recently deployed the Bioportal appliance to one of our AWS environments but can?t seem to login using the credentials: Username: admin Password: changemeNOW Whenever I try I get the error: ?Errors On Form. Invalid account name/password combination? The default ssh user credentials worked and I can confirm ssh access. I can also confirm that creating a new user and uploading an ontology works, so good news there ? The process I followed to deploy this appliance is as follows: 1. Download OVA image from https://bioportal.bioontology.org/virtual_appliance 2. Copy OVA to s3 bucket 3. Use aws cli to convert image to AMI as detailed here 4. Launched virtual machine using the converted AMI 5. Navigate to portal 6. Try to login as admin 7. Get error Can you please confirm that the credentials I?m trying to use are correct? And is there a way to reset the ?admin? user?s password? Thanks, Alex. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jgraybeal at stanford.edu Thu Jul 23 09:06:42 2020 From: jgraybeal at stanford.edu (John Graybeal) Date: Thu, 23 Jul 2020 16:06:42 +0000 Subject: [bioontology-support] Databiology: Default web portal credentials In-Reply-To: References: Message-ID: <7D167CAD-398C-478F-9727-C063F6972F4E@stanford.edu> Hi Alex, Thanks for the note about the license key, I've approved your license. Please let me know if you don't get the email, we're working through some email issues. It sounds like the ontology parsing didn't complete successfully. The guidance in the Submitting Ontologies and Troubleshooting Submissions sections of our Administration guide might help you to narrow down the problem. (The most common problem we see in BioPortal is that the ontology isn't parseable, and that can be checked with Protege, but you may have checked that already.) If that doesn't work, let us know where you get stuck. John On Jul 22, 2020, at 11:02 PM, Alex Mozejko > wrote: Hi Alex, Apologies for taking so long to get back to you on this. Thank you very much to the ?firstboot? tip, that worked a treat. A couple of weeks ago I created a request at https://license.ontoportal.org/licenses for appliance id d8d04b7b-577b-4d09-b40a-82ccc0a12b99. Can you please double check that this hasn?t been lost? I?m happy to provide additional information if required. Also we?re having issues loading new Ontologies, we can use the portal to upload a file and it appears in the list however when clicking into the Ontology, the summary tab shows: Metrics We have not yet calculated metrics for ONTOLOGY Visits We are still collecting data for ONTOLOGY And the ?classes? tab reports: ?Problem retrieving classes? Does any of this sound familiar? Or can you suggest some logs to read which might point us in a right direction to solve? Apologies again for taking so long to respond. Thanks, Alex. From: Alex Skrenchuk > Sent: Friday, 3 July 2020 5:42 AM To: Alex Mozejko >; support at bioontology.org Subject: Re: [bioontology-support] Databiology: Default web portal credentials HI Alex, We have not yet experimented with importing OVA to AWS because we are counting that the majority of users will deploy OntoPortal from the AWS marketplace. We were recently been made aware that version 3.0.1 of the appliance sometimes doesn?t initialize properly in AWS during the first boot which could be usually resolved with a second reboot. During the very first boot of the appliance we have a firstboot script that resets API keys for the Web UI and Admin user. If it detects that appliance is running in AWS then it will also resets Admin password to match the instance-id of your EC2 instance. First I would try to use the EC2 instance-id for admin password and if that doesn?t work then you could try to force re-run of the firstboot script. ssh to instance as centos user and: sudo touch /srv/ontoportal/firstboot sudo chown ontoportal /srv/ontoportal/firstboot sudo reboot -Alex From: bioontology-support > on behalf of Alex Mozejko > Date: Thursday, July 2, 2020 at 8:00 AM To: "support at bioontology.org" > Subject: [bioontology-support] Databiology: Default web portal credentials Hello, We have recently deployed the Bioportal appliance to one of our AWS environments but can?t seem to login using the credentials: Username: admin Password: changemeNOW Whenever I try I get the error: ?Errors On Form. Invalid account name/password combination? The default ssh user credentials worked and I can confirm ssh access. I can also confirm that creating a new user and uploading an ontology works, so good news there ? The process I followed to deploy this appliance is as follows: 1. Download OVA image from https://bioportal.bioontology.org/virtual_appliance 2. Copy OVA to s3 bucket 3. Use aws cli to convert image to AMI as detailed here 4. Launched virtual machine using the converted AMI 5. Navigate to portal 6. Try to login as admin 7. Get error Can you please confirm that the credentials I?m trying to use are correct? And is there a way to reset the ?admin? user?s password? Thanks, Alex. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From clair.kronk at gmail.com Thu Jul 23 12:58:00 2020 From: clair.kronk at gmail.com (superraptor2) Date: Thu, 23 Jul 2020 14:58:00 -0500 (CDT) Subject: [bioontology-support] Getting IDs to resolve correctly with the GSSO Message-ID: <1595534280745-0.post@n4.nabble.com> Hi! I'm attempting to log the GSSO with a prefix at identifiers.org and part of that process requires agnostic identifiers. Basically, when I applied, the GSSO resolved individual identifiers with URLs such as http://purl.bioontology.org/ontology/GSSO?p=classes&conceptid=http://purl.bioontology.org/ontology/GSSO/000096 instead of http://purl.bioontology.org/ontology/GSSO/GSSO:000096. I attempted to update this from 2.0.0 to 2.0.1, changing the IDs from http://purl.bioontology.org/ontology/GSSO/000096 to http://purl.bioontology.org/ontology/GSSO/GSSO_006778, in order to mimic those at the Gene Ontology, but it still requires something like http://bioportal.bioontology.org/ontologies/GSSO/?p=classes&conceptid=http://purl.bioontology.org/ontology/GSSO/GSSO_006778 instead of http://bioportal.bioontology.org/ontologies/GSSO/GSSO:006778 or http://bioportal.bioontology.org/ontologies/GSSO/GSSO_006778. What's the best/fastest way to resolve these URLs? i.e. what do I need to change within the annotations themselves for this to work? I'm editing ~12,000 entries via Protege, so anything I can do non-manually and in bulk would be incredibly useful! Thanks so much! -- Sent from: http://ncbo-support.2288202.n4.nabble.com/ From alex.mozejko at databiology.com Fri Jul 24 03:00:41 2020 From: alex.mozejko at databiology.com (Alex Mozejko) Date: Fri, 24 Jul 2020 10:00:41 +0000 Subject: [bioontology-support] Databiology: Default web portal credentials In-Reply-To: <7D167CAD-398C-478F-9727-C063F6972F4E@stanford.edu> References: <7D167CAD-398C-478F-9727-C063F6972F4E@stanford.edu> Message-ID: Hi John, Thanks for organising the license. I can confirm that the email came through (albeit to ?junk? ?) and that the license was able to be applied successfully. Thanks also for the troubleshooting tips, I haven?t had a chance to look through these today but hopefully will be able to early next week. Thanks, Alex. From: John Graybeal Sent: Friday, 24 July 2020 12:07 AM To: Alex Mozejko Cc: Alex Skrenchuk ; support at bioontology.org; Georges Heiter Subject: Re: [bioontology-support] Databiology: Default web portal credentials Hi Alex, Thanks for the note about the license key, I've approved your license. Please let me know if you don't get the email, we're working through some email issues. It sounds like the ontology parsing didn't complete successfully. The guidance in the Submitting Ontologies and Troubleshooting Submissions sections of our Administration guide might help you to narrow down the problem. (The most common problem we see in BioPortal is that the ontology isn't parseable, and that can be checked with Protege, but you may have checked that already.) If that doesn't work, let us know where you get stuck. John On Jul 22, 2020, at 11:02 PM, Alex Mozejko > wrote: Hi Alex, Apologies for taking so long to get back to you on this. Thank you very much to the ?firstboot? tip, that worked a treat. A couple of weeks ago I created a request at https://license.ontoportal.org/licenses for appliance id d8d04b7b-577b-4d09-b40a-82ccc0a12b99. Can you please double check that this hasn?t been lost? I?m happy to provide additional information if required. Also we?re having issues loading new Ontologies, we can use the portal to upload a file and it appears in the list however when clicking into the Ontology, the summary tab shows: Metrics We have not yet calculated metrics for ONTOLOGY Visits We are still collecting data for ONTOLOGY And the ?classes? tab reports: ?Problem retrieving classes? Does any of this sound familiar? Or can you suggest some logs to read which might point us in a right direction to solve? Apologies again for taking so long to respond. Thanks, Alex. From: Alex Skrenchuk > Sent: Friday, 3 July 2020 5:42 AM To: Alex Mozejko >; support at bioontology.org Subject: Re: [bioontology-support] Databiology: Default web portal credentials HI Alex, We have not yet experimented with importing OVA to AWS because we are counting that the majority of users will deploy OntoPortal from the AWS marketplace. We were recently been made aware that version 3.0.1 of the appliance sometimes doesn?t initialize properly in AWS during the first boot which could be usually resolved with a second reboot. During the very first boot of the appliance we have a firstboot script that resets API keys for the Web UI and Admin user. If it detects that appliance is running in AWS then it will also resets Admin password to match the instance-id of your EC2 instance. First I would try to use the EC2 instance-id for admin password and if that doesn?t work then you could try to force re-run of the firstboot script. ssh to instance as centos user and: sudo touch /srv/ontoportal/firstboot sudo chown ontoportal /srv/ontoportal/firstboot sudo reboot -Alex From: bioontology-support > on behalf of Alex Mozejko > Date: Thursday, July 2, 2020 at 8:00 AM To: "support at bioontology.org" > Subject: [bioontology-support] Databiology: Default web portal credentials Hello, We have recently deployed the Bioportal appliance to one of our AWS environments but can?t seem to login using the credentials: Username: admin Password: changemeNOW Whenever I try I get the error: ?Errors On Form. Invalid account name/password combination? The default ssh user credentials worked and I can confirm ssh access. I can also confirm that creating a new user and uploading an ontology works, so good news there ? The process I followed to deploy this appliance is as follows: 1. Download OVA image from https://bioportal.bioontology.org/virtual_appliance 2. Copy OVA to s3 bucket 3. Use aws cli to convert image to AMI as detailed here 4. Launched virtual machine using the converted AMI 5. Navigate to portal 6. Try to login as admin 7. Get error Can you please confirm that the credentials I?m trying to use are correct? And is there a way to reset the ?admin? user?s password? Thanks, Alex. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support ======================== John Graybeal Technical Program Manager Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal Stanford Center for Biomedical Informatics Research 650-736-1632 | ORCID 0000-0001-6875-5360 -------------- next part -------------- An HTML attachment was scrubbed... URL: From coss at cnb.csic.es Thu Jul 23 22:43:48 2020 From: coss at cnb.csic.es (Carlos Oscar Sorzano) Date: Fri, 24 Jul 2020 07:43:48 +0200 Subject: [bioontology-support] Problem retrieving classes Message-ID: <65350038-9387-d5f9-269a-0e8c74c2e7ba@cnb.csic.es> Dear colleagues, I uploaded yesterday an ontology file for Cryo Electron Microscopy (http://bioportal.bioontology.org/ontologies/CRYOEM/?p=classes&conceptid=root). The OWL file was generated with Protege and it does not show any obvious error in Protege. However, when it is read at BioPortal there is some problem because we see the error message "Problem retrieving classes" (see previous link). The file is partly parsed because it shows some metrics, but we must have something wrong with the file. Could you help us with any hint? Kind regards and thanks, Carlos Oscar From vendetti at stanford.edu Fri Jul 24 11:30:28 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 24 Jul 2020 18:30:28 +0000 Subject: [bioontology-support] Getting IDs to resolve correctly with the GSSO In-Reply-To: <1595534280745-0.post@n4.nabble.com> References: <1595534280745-0.post@n4.nabble.com> Message-ID: <6D1EF297-EAD2-4D0A-AEB4-0DFCE7C41635@stanford.edu> Hello, I started looking into this yesterday evening, and I?m not sure I have a complete answer for you yet. When end users submit ontologies to BioPortal, an ontology PURL is created using this format: http://purl.bioontology.org/ontology/GSSO ? where your ontology acronym makes up the last fragment of the PURL. If you enter that PURL in a browser address bar, the BioPortal PURL server will resolve it to the following URL pattern: http://bioportal.bioontology.org/ontologies/GSSO This is the home page for your ontology in the BioPortal web application (developed in Ruby on Rails). If you want a permanent link to any given class in your ontology that will resolve to the corresponding page in the BioPortal web application, you can use a URL pattern where you tack the URL encoded class ID onto the end of the ontology PURL using the ?conceptid=? parameter in the query string. For example, the permanent link to the ?transgender? class from your GSSO ontology would be the following: http://purl.bioontology.org/ontology/GSSO?conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FGSSO%2FGSSO_000096 I did find an exception to the above information that occurs with all of the UMLS format ontologies in BioPortal, e.g., SNOMEDCT, etc. These ontologies are bulk-imported into BioPortal twice per year using a custom process that writes the ontology data directly into the RDF store, bypassing the file upload process normally performed by end users. For these ontologies, several formats for permanent class links work, e.g., all of the following PURLS will resolve to the ?Body structure? class in the SNOMEDCT ontology: http://purl.bioontology.org/ontology/SNOMEDCT/123037004 http://purl.bioontology.org/ontology/SNOMEDCT?conceptid=123037004 http://purl.bioontology.org/ontology/SNOMEDCT?conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F123037004 I?m not yet able to provide more details about why this only works for UMLS format ontologies. You mentioned that you?re editing a large number of entries in Protege. I?m not sure if you?re aware that we provide a REST API for programmatic retrieval of ontology data, documented here: http://data.bioontology.org/documentation. For example, you could retrieve data about the ?transgender? class using the following REST call: http://data.bioontology.org/ontologies/GSSO/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FGSSO%2FGSSO_000096 It?s a hypermedia API, and one of the links returned is a ?ui? link with a URL that navigates to the page for said class in the BioPortal web application (http://bioportal.bioontology.org/ontologies/GSSO?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FGSSO%2FGSSO_000096). We provide examples of using the API in several languages in one of our GitHub repositories: https://github.com/ncbo/ncbo_rest_sample_code. Hope this information is helpful. Kind regards, Jennifer [cid:385A57B1-A516-4F52-A9F3-C0422509D101 at stanford.edu] On Jul 23, 2020, at 12:58 PM, superraptor2 > wrote: Hi! I'm attempting to log the GSSO with a prefix at identifiers.org and part of that process requires agnostic identifiers. Basically, when I applied, the GSSO resolved individual identifiers with URLs such as http://purl.bioontology.org/ontology/GSSO?p=classes&conceptid=http://purl.bioontology.org/ontology/GSSO/000096 instead of http://purl.bioontology.org/ontology/GSSO/GSSO:000096. I attempted to update this from 2.0.0 to 2.0.1, changing the IDs from http://purl.bioontology.org/ontology/GSSO/000096 to http://purl.bioontology.org/ontology/GSSO/GSSO_006778, in order to mimic those at the Gene Ontology, but it still requires something like http://bioportal.bioontology.org/ontologies/GSSO/?p=classes&conceptid=http://purl.bioontology.org/ontology/GSSO/GSSO_006778 instead of http://bioportal.bioontology.org/ontologies/GSSO/GSSO:006778 or http://bioportal.bioontology.org/ontologies/GSSO/GSSO_006778. What's the best/fastest way to resolve these URLs? i.e. what do I need to change within the annotations themselves for this to work? I'm editing ~12,000 entries via Protege, so anything I can do non-manually and in bulk would be incredibly useful! Thanks so much! -- Sent from: http://ncbo-support.2288202.n4.nabble.com/ _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2020-07-24 11.23.10.png Type: image/png Size: 242536 bytes Desc: Screenshot 2020-07-24 11.23.10.png URL: From vendetti at stanford.edu Fri Jul 24 11:53:48 2020 From: vendetti at stanford.edu (Jennifer Leigh Vendetti) Date: Fri, 24 Jul 2020 18:53:48 +0000 Subject: [bioontology-support] Problem retrieving classes In-Reply-To: <65350038-9387-d5f9-269a-0e8c74c2e7ba@cnb.csic.es> References: <65350038-9387-d5f9-269a-0e8c74c2e7ba@cnb.csic.es> Message-ID: <15D2C6A1-C747-4738-896A-B97FDC9E1F2E@stanford.edu> Hello Carlos Oscar, I looked at the contents of your ontology source file. You mentioned that it?s an OWL file, but the contents appear to be in OBO format, i.e., see the following snippet from the top of your ontology showing OBO-style term stanzas: format-version: 1.2 ontology: http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2 owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(AnnotationProperty())\n\n\nAnnotationAssertion( \"ProtProcessMovies\"^^xsd:string)\n) [Term] id: Acquisition comment: Contains acquisition parameters such as magnification, voltage, spherical aberration, amplitude contrast, dose per frame and inital dose, optics group, and beam tilt is_a: EMObject [Term] id: AtomStruct comment: File representing an atomic structure (PDB, mmCIF, ...) is_a: EMObject property_value: hasVolume "Volume" The first line indicates that the ontology file is written in OBO format version 1.2, however the rest of the header tags aren?t valid according to OBO file format documentation here: https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html#S.2.1 Could you provide more detail about how this ontology was generated? Do you have an OBO source file that you attempted to convert to a different format using the Protege desktop application? Also, I do see an error message in the Protege log when opening your ontology in the desktop version (Window -> Show log?). [cid:810EFD70-59D3-4894-8185-3BC4CF96DC3E at stanford.edu] Kind regards, Jennifer On Jul 23, 2020, at 10:43 PM, Carlos Oscar Sorzano > wrote: Dear colleagues, I uploaded yesterday an ontology file for Cryo Electron Microscopy (http://bioportal.bioontology.org/ontologies/CRYOEM/?p=classes&conceptid=root). The OWL file was generated with Protege and it does not show any obvious error in Protege. However, when it is read at BioPortal there is some problem because we see the error message "Problem retrieving classes" (see previous link). The file is partly parsed because it shows some metrics, but we must have something wrong with the file. Could you help us with any hint? Kind regards and thanks, Carlos Oscar _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2020-07-24 11.52.33.png Type: image/png Size: 448373 bytes Desc: Screenshot 2020-07-24 11.52.33.png URL: From support at bioontology.org Sun Jul 26 22:47:27 2020 From: support at bioontology.org (support at bioontology.org) Date: Sun, 26 Jul 2020 22:47:27 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Farid Message-ID: <5f1e6a6f9d191_65e120eb0bc70533@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From coss at cnb.csic.es Sat Jul 25 01:13:41 2020 From: coss at cnb.csic.es (Carlos Oscar Sorzano) Date: Sat, 25 Jul 2020 10:13:41 +0200 Subject: [bioontology-support] Problem retrieving classes In-Reply-To: <15D2C6A1-C747-4738-896A-B97FDC9E1F2E@stanford.edu> References: <65350038-9387-d5f9-269a-0e8c74c2e7ba@cnb.csic.es> <15D2C6A1-C747-4738-896A-B97FDC9E1F2E@stanford.edu> Message-ID: Thank you, Jennifer. I will check the configuration of Protege and see if I can save a truly OWL file. At least I have now something to look at. Kind regards, Carlos Oscar El 24/07/2020 a las 20:53, Jennifer Leigh Vendetti escribi?: > Hello Carlos Oscar, > > I looked at the contents of your ontology source file. You mentioned > that it?s an OWL file, but the contents appear to be in OBO format, > i.e., see the following snippet from the top of your ontology showing > OBO-style term stanzas: > > format-version: 1.2 > ontology: > http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2 > owl-axioms: > Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(AnnotationProperty())\n\n\nAnnotationAssertion( > > \"ProtProcessMovies\"^^xsd:string)\n) > > [Term] > id: Acquisition > comment: Contains acquisition parameters such as magnification, > voltage, spherical aberration, amplitude contrast, dose per frame and > inital dose, optics group, and beam tilt > is_a: EMObject > > [Term] > id: AtomStruct > comment: File representing an atomic structure (PDB, mmCIF, ...) > is_a: EMObject > property_value: hasVolume "Volume" > > The first line indicates that the ontology file is written in OBO > format version 1.2, however the rest of the header tags aren?t valid > according to OBO file format documentation here: > > https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html#S.2.1 > > Could you provide more detail about how this ontology was generated? > Do you have an OBO source file that you attempted to convert to a > different format using the Protege desktop application? Also, I do see > an error message in the Protege log when opening your ontology in the > desktop version (Window -> Show log?). > > > Kind regards, > Jennifer > > >> On Jul 23, 2020, at 10:43 PM, Carlos Oscar Sorzano > > wrote: >> >> Dear colleagues, >> >> I uploaded yesterday an ontology file for Cryo Electron Microscopy >> (http://bioportal.bioontology.org/ontologies/CRYOEM/?p=classes&conceptid=root). >> The OWL file was generated with Protege and it does not show any >> obvious error in Protege. However, when it is read at BioPortal there >> is some problem because we see the error message "Problem retrieving >> classes" (see previous link). The file is partly parsed because it >> shows some metrics, but we must have something wrong with the file. >> Could you help us with any hint? >> >> Kind regards and thanks, Carlos Oscar >> _______________________________________________ >> bioontology-support mailing list >> bioontology-support at lists.stanford.edu >> >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2020-07-24 11.52.33.png Type: image/png Size: 448373 bytes Desc: not available URL: From support at bioontology.org Mon Jul 27 03:50:49 2020 From: support at bioontology.org (support at bioontology.org) Date: Mon, 27 Jul 2020 03:50:49 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Marwa Message-ID: <5f1eb189b7697_6a51274577850840@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Mon Jul 27 13:25:28 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Mon, 27 Jul 2020 20:25:28 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Marwa In-Reply-To: <5f1eb189b7697_6a51274577850840@ncbo-prd-app-09.stanford.edu.mail> References: <5f1eb189b7697_6a51274577850840@ncbo-prd-app-09.stanford.edu.mail> Message-ID: Hi Marwa, Thank you for your questions. In BioPortal there are optional categories that one can assign to his/her ontology during the creation phase. An ontology can belong to multiple categories, but they are not hierarchical. You can obtain the list of available categories by using this API service endpoint: http://data.bioontology.org/categories To determine which group an ontology belongs to, you can make this call: http://data.bioontology.org/ontologies/SNOMEDCT?display=all The ?hasDomain? field contains the list of the categories for a given ontology. To your second question, our current data store is an RDF database called ?4store?: https://github.com/4store/4store We do, however, have short-term plans to migrate to AllegroGraph: https://allegrograph.com/products/allegrograph/ Our Virtual Appliance v3.0, which you can download and install in your own environment, already includes compatibility with AllegroGraph. As far the direct access to the database, we have a SPARQL endpoint that you can use: http://sparql.bioontology.org/ Unfortunately, the data contained in that endpoint isn?t regularly synced with our production data, so it will not contain all the ontologies that exist in BioPortal. As part of the near future migration to AllegroGraph, we plan to implement a SPARQL endpoint that mirrors our production data. Please let me know if I omitted anything or if you have further questions. Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On Jul 27, 2020, at 3:50 AM, support at bioontology.org wrote: Name: Marwa Email: marwa.abdelrehem at fci.au.edu.eg Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies Feedback: I am a researcher interested in ontology reuse and especially in bio-ontologies. In a part of my research, I am interested to determine the ontology domain (Category). My question is does bioportal has a hierarchy for those categories? and if so, can I have access to it? The second question is what is the type of database that you store the ontologies information in? and also can I have access to it? Thanks in advance. _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Mon Jul 27 16:17:03 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Mon, 27 Jul 2020 23:17:03 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Farid In-Reply-To: <5f1e6a6f9d191_65e120eb0bc70533@ncbo-prd-app-09.stanford.edu.mail> References: <5f1e6a6f9d191_65e120eb0bc70533@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <0CA80811-B45C-49EE-B908-A07B8DF036D7@stanford.edu> Hi Farid, Thank you for your inquiry. I am not an ontology expert, but you can look at a few ontologies, such as: Human Disease Ontology (DOID) https://bioportal.bioontology.org/ontologies/DOID Foundational Model of Anatomy (FMA) https://bioportal.bioontology.org/ontologies/FMA The Clinical Terms Ontology (SNOMEDCT) https://bioportal.bioontology.org/ontologies/SNOMEDCT Medical Dictionary for Regulatory Activities Terminology (MedDRA) https://bioportal.bioontology.org/ontologies/MEDDRA If you have a specific text that you need to match against the most relevant ontologies, you can use our Ontology Recommender service: https://bioportal.bioontology.org/recommender Based on your text, the Recommender finds ontologies that are best suited for the terms found in that text. You can also use the Category filter on the Ontologies page to narrow the list down to ontologies you deem the most relevant: https://bioportal.bioontology.org/ontologies You can access any of these ontologies or tools using our REST API services. The usage instructions can be found here: http://data.bioontology.org/documentation Thanks, Michael ---------------------------------------------------- Michael Dorf Chief Software Architect The National Center for Biomedical Ontology Stanford Biomedical Informatics Research mdorf at stanford.edu O: 650-723-0357 M: 650-995-4374 ---------------------------------------------------- On Jul 26, 2020, at 10:47 PM, support at bioontology.org wrote: Name: Farid Email: ismayilzadeh.farid at gmail.com Location: https%3A%2F%2Fbioportal.bioontology.org%2Fannotator Feedback: Hi. I am looking for a dataset that include list of all diseases, categories, body types, causes and symptoms. Can i get these data from you ? Best regards Farid Ismayilzada _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From coss at cnb.csic.es Tue Jul 28 04:25:29 2020 From: coss at cnb.csic.es (Carlos Oscar Sorzano) Date: Tue, 28 Jul 2020 13:25:29 +0200 Subject: [bioontology-support] Problem retrieving classes In-Reply-To: <15D2C6A1-C747-4738-896A-B97FDC9E1F2E@stanford.edu> References: <65350038-9387-d5f9-269a-0e8c74c2e7ba@cnb.csic.es> <15D2C6A1-C747-4738-896A-B97FDC9E1F2E@stanford.edu> Message-ID: <5bfb1388-7c1b-0848-87db-d063c8a72909@cnb.csic.es> Dear Jennifer, presumably I have uploaded now a true OWL file, but BioPortal cannot show yet the classes. Would you mind having a look? And thank you very much. Kind regards, Carlos Oscar On 7/24/20 8:53 PM, Jennifer Leigh Vendetti wrote: > Hello Carlos Oscar, > > I looked at the contents of your ontology source file. You mentioned > that it?s an OWL file, but the contents appear to be in OBO format, > i.e., see the following snippet from the top of your ontology showing > OBO-style term stanzas: > > format-version: 1.2 > ontology: > http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2 > owl-axioms: > Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(AnnotationProperty())\n\n\nAnnotationAssertion( > > \"ProtProcessMovies\"^^xsd:string)\n) > > [Term] > id: Acquisition > comment: Contains acquisition parameters such as magnification, > voltage, spherical aberration, amplitude contrast, dose per frame and > inital dose, optics group, and beam tilt > is_a: EMObject > > [Term] > id: AtomStruct > comment: File representing an atomic structure (PDB, mmCIF, ...) > is_a: EMObject > property_value: hasVolume "Volume" > > The first line indicates that the ontology file is written in OBO > format version 1.2, however the rest of the header tags aren?t valid > according to OBO file format documentation here: > > https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html#S.2.1 > > Could you provide more detail about how this ontology was generated? > Do you have an OBO source file that you attempted to convert to a > different format using the Protege desktop application? Also, I do see > an error message in the Protege log when opening your ontology in the > desktop version (Window -> Show log?). > > > Kind regards, > Jennifer > > >> On Jul 23, 2020, at 10:43 PM, Carlos Oscar Sorzano > > wrote: >> >> Dear colleagues, >> >> I uploaded yesterday an ontology file for Cryo Electron Microscopy >> (http://bioportal.bioontology.org/ontologies/CRYOEM/?p=classes&conceptid=root). >> The OWL file was generated with Protege and it does not show any >> obvious error in Protege. However, when it is read at BioPortal there >> is some problem because we see the error message "Problem retrieving >> classes" (see previous link). The file is partly parsed because it >> shows some metrics, but we must have something wrong with the file. >> Could you help us with any hint? >> >> Kind regards and thanks, Carlos Oscar >> _______________________________________________ >> bioontology-support mailing list >> bioontology-support at lists.stanford.edu >> >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2020-07-24 11.52.33.png Type: image/png Size: 448373 bytes Desc: not available URL: From support at bioontology.org Tue Jul 28 04:52:07 2020 From: support at bioontology.org (support at bioontology.org) Date: Tue, 28 Jul 2020 04:52:07 -0700 Subject: [bioontology-support] [BioPortal] Feedback from Emma Vos Message-ID: <5f201167d183c_1d3c1b2da1c8797@ncbo-prd-app-09.stanford.edu.mail> An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue Jul 28 09:13:09 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 28 Jul 2020 16:13:09 +0000 Subject: [bioontology-support] Problem retrieving classes In-Reply-To: <5bfb1388-7c1b-0848-87db-d063c8a72909@cnb.csic.es> References: <65350038-9387-d5f9-269a-0e8c74c2e7ba@cnb.csic.es> <15D2C6A1-C747-4738-896A-B97FDC9E1F2E@stanford.edu> <5bfb1388-7c1b-0848-87db-d063c8a72909@cnb.csic.es> Message-ID: <8615803C-0030-42E0-B6AA-8B2CEF22060A@stanford.edu> Hi Carlos, It looks like the ontology has loaded correctly, but it hasn?t had a chance to propagate through our caching layers. I?ve cleared the system caches manually, and the ontology now appears and functions correctly. Let me know if you are still seeing any issues. Thank you, Michael On Jul 28, 2020, at 4:25 AM, Carlos Oscar Sorzano > wrote: Dear Jennifer, presumably I have uploaded now a true OWL file, but BioPortal cannot show yet the classes. Would you mind having a look? And thank you very much. Kind regards, Carlos Oscar On 7/24/20 8:53 PM, Jennifer Leigh Vendetti wrote: Hello Carlos Oscar, I looked at the contents of your ontology source file. You mentioned that it?s an OWL file, but the contents appear to be in OBO format, i.e., see the following snippet from the top of your ontology showing OBO-style term stanzas: format-version: 1.2 ontology: http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2 owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(AnnotationProperty())\n\n\nAnnotationAssertion( \"ProtProcessMovies\"^^xsd:string)\n) [Term] id: Acquisition comment: Contains acquisition parameters such as magnification, voltage, spherical aberration, amplitude contrast, dose per frame and inital dose, optics group, and beam tilt is_a: EMObject [Term] id: AtomStruct comment: File representing an atomic structure (PDB, mmCIF, ...) is_a: EMObject property_value: hasVolume "Volume" The first line indicates that the ontology file is written in OBO format version 1.2, however the rest of the header tags aren?t valid according to OBO file format documentation here: https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html#S.2.1 Could you provide more detail about how this ontology was generated? Do you have an OBO source file that you attempted to convert to a different format using the Protege desktop application? Also, I do see an error message in the Protege log when opening your ontology in the desktop version (Window -> Show log?). Kind regards, Jennifer On Jul 23, 2020, at 10:43 PM, Carlos Oscar Sorzano > wrote: Dear colleagues, I uploaded yesterday an ontology file for Cryo Electron Microscopy (http://bioportal.bioontology.org/ontologies/CRYOEM/?p=classes&conceptid=root). The OWL file was generated with Protege and it does not show any obvious error in Protege. However, when it is read at BioPortal there is some problem because we see the error message "Problem retrieving classes" (see previous link). The file is partly parsed because it shows some metrics, but we must have something wrong with the file. Could you help us with any hint? Kind regards and thanks, Carlos Oscar _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From mdorf at stanford.edu Tue Jul 28 13:24:46 2020 From: mdorf at stanford.edu (Michael Dorf) Date: Tue, 28 Jul 2020 20:24:46 +0000 Subject: [bioontology-support] [BioPortal] Feedback from Emma Vos In-Reply-To: <5f201167d183c_1d3c1b2da1c8797@ncbo-prd-app-09.stanford.edu.mail> References: <5f201167d183c_1d3c1b2da1c8797@ncbo-prd-app-09.stanford.edu.mail> Message-ID: <2690D207-8E73-409D-96F5-1584823EC6C9@stanford.edu> Hi Emma, Thank you for your question. The "display=all? query parameter will give you the info you need: http://data.bioontology.org/ontologies/CL/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000576?display=all Let me know if you require further assistance. Michael On Jul 28, 2020, at 4:52 AM, support at bioontology.org wrote: Name: Emma Vos Email: emma at thehyve.nl Location: https%3A%2F%2Fbioportal.bioontology.org%2Fannotator Feedback: Dear BioPortal support, I have a question about the API. I would like to get the prefixIRI of a term, like CL:000576 in https://bioportal.bioontology.org/ontologies/CL?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000576. But when accessing the data through the API (http://data.bioontology.org/ontologies/CL/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000576), I see some of the attributes of this term (like prefLabel and definition), but prefixIRI is missing from the attributes. I have read the API documentation, but it is not completely clear to me how I can get other attributes like prefixIRI. Could you potentially help me out with this? Kind regards, Emma Vos _______________________________________________ bioontology-support mailing list bioontology-support at lists.stanford.edu https://mailman.stanford.edu/mailman/listinfo/bioontology-support -------------- next part -------------- An HTML attachment was scrubbed... URL: From coss at cnb.csic.es Tue Jul 28 08:04:53 2020 From: coss at cnb.csic.es (Carlos Oscar Sorzano) Date: Tue, 28 Jul 2020 17:04:53 +0200 Subject: [bioontology-support] Problem retrieving classes In-Reply-To: <8615803C-0030-42E0-B6AA-8B2CEF22060A@stanford.edu> References: <65350038-9387-d5f9-269a-0e8c74c2e7ba@cnb.csic.es> <15D2C6A1-C747-4738-896A-B97FDC9E1F2E@stanford.edu> <5bfb1388-7c1b-0848-87db-d063c8a72909@cnb.csic.es> <8615803C-0030-42E0-B6AA-8B2CEF22060A@stanford.edu> Message-ID: Thank you very much, it really worked. Kind regards, Carlos Oscar El 28/07/2020 a las 18:13, Michael Dorf escribi?: > Hi Carlos, > > It looks like the ontology has loaded correctly, but it hasn?t had a > chance to propagate through our caching layers. I?ve cleared the > system caches manually, and the ontology now appears and functions > correctly. > > Let me know if you are still seeing any issues. > > Thank you, > > Michael > > > > >> On Jul 28, 2020, at 4:25 AM, Carlos Oscar Sorzano > > wrote: >> >> Dear Jennifer, >> >> presumably I have uploaded now a true OWL file, but BioPortal cannot >> show yet the classes. Would you mind having a look? And thank you >> very much. >> >> Kind regards, Carlos Oscar >> >> On 7/24/20 8:53 PM, Jennifer Leigh Vendetti wrote: >>> Hello Carlos Oscar, >>> >>> I looked at the contents of your ontology source file. You mentioned >>> that it?s an OWL file, but the contents appear to be in OBO format, >>> i.e., see the following snippet from the top of your ontology >>> showing OBO-style term stanzas: >>> >>> format-version: 1.2 >>> ontology: >>> http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2 >>> owl-axioms: >>> Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(AnnotationProperty())\n\n\nAnnotationAssertion( >>> >>> \"ProtProcessMovies\"^^xsd:string)\n) >>> >>> [Term] >>> id: Acquisition >>> comment: Contains acquisition parameters such as magnification, >>> voltage, spherical aberration, amplitude contrast, dose per frame >>> and inital dose, optics group, and beam tilt >>> is_a: EMObject >>> >>> [Term] >>> id: AtomStruct >>> comment: File representing an atomic structure (PDB, mmCIF, ...) >>> is_a: EMObject >>> property_value: hasVolume "Volume" >>> >>> The first line indicates that the ontology file is written in OBO >>> format version 1.2, however the rest of the header tags aren?t valid >>> according to OBO file format documentation here: >>> >>> https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html#S.2.1 >>> >>> Could you provide more detail about how this ontology was generated? >>> Do you have an OBO source file that you attempted to convert to a >>> different format using the Protege desktop application? Also, I do >>> see an error message in the Protege log when opening your ontology >>> in the desktop version (Window -> Show log?). >>> >>> >>> >>> Kind regards, >>> Jennifer >>> >>> >>>> On Jul 23, 2020, at 10:43 PM, Carlos Oscar Sorzano >>>> > wrote: >>>> >>>> Dear colleagues, >>>> >>>> I uploaded yesterday an ontology file for Cryo Electron Microscopy >>>> (http://bioportal.bioontology.org/ontologies/CRYOEM/?p=classes&conceptid=root). >>>> The OWL file was generated with Protege and it does not show any >>>> obvious error in Protege. However, when it is read at BioPortal >>>> there is some problem because we see the error message "Problem >>>> retrieving classes" (see previous link). The file is partly parsed >>>> because it shows some metrics, but we must have something wrong >>>> with the file. Could you help us with any hint? >>>> >>>> Kind regards and thanks, Carlos Oscar >>>> _______________________________________________ >>>> bioontology-support mailing list >>>> bioontology-support at lists.stanford.edu >>>> >>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support >>> >> _______________________________________________ >> bioontology-support mailing list >> bioontology-support at lists.stanford.edu >> >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support > -------------- next part -------------- An HTML attachment was scrubbed... URL: