Poster for OpenPLant

[gilienv]

Have made changes to Google Doc. Please check

[petermr]

Attention ALL! We now need to start creating the poster. This is an International Meeting so it's is a great advertisement for you and EssoilDB. As always quality is the most important thing.

We should ALL contribute to the creation of the poster, but remember that the space is limited, so short clear sentences and diagrams are the most likely to be valuable. A diagram is almost always better than words.

What OpenPlant people will want to know is:

• what is EssoilDB?
• why is it important?
• what is in it (as much detail compatible with clarity - this is hard!)?
• how can I use it? (also hard)
• how can I get more information? (and add more ideas here)

Some delegates take a quick look at a poster and then decide whether it's worth looking at in more detail. Others spend a long time looking at details.

has anyone besides Gita and me contributed to a paper or a poster? If it's your first time here are some ideas. https://uofgpgrblog.com/pgrblog/how-to-impress-with-your-conference-research-poster-2 https://ugs.utexas.edu/our/poster/samples https://blogs.lse.ac.uk/impactofsocialsciences/2018/05/11/how-to-design-an-award-winning-conference-poster/

These include many of the basics:

• clear flow of information
• limit word count
• make the poster engaging
• things not to forget (like authors and affiliations!) and logos

I'd suggest:

• We use a communally editable Googledoc for the initial components.
• we immediately start on (a) narrative (story) and (b) listing the components
• we make sure we have the easiest critical parts ready as soon as possible (e.g. the header, photos, references, etc,

The work can be do in parallel. So I'd suggest we have: 1 why EssoilDB is exciting and valuable. Vinita and Shruthi 2 what the new structure contains (13 tables) (Manish and Ambarish).

I think 1 will benefit from some Indian examples (e.g. phytochemical production and harvesting of terpenes (spices, fragrances, medicine,) or pheromones . This is a great chance to set the scene with photos. NOTE: all photos MUST have CC BY licences and attribution. Wikimedia is a good place to do this, but NIPGR may also have photos.

2 could start with an Entity Relation diagram of the main tables. Also an example of the data in the main tables (plants, compounds, profiles). This could be the central part of the poster, with each table decorated with example of its contents.

The main story is:

• read a paper
• extract the profile
• identify the plant, and its parameters (e.g. seed)
• identify the compound/s
• search the database and/or Linked Open Database.

NOTE: This should be YOUR poster, with me acting as mentor. Say what you want to say, and then we'll communally hack it into shape. At the end of this will be a poster that YOU can be proud of, put on your lab/home wall, see displayed at NIPGR, etc.

[Shruthi-M]

These were the key-points discussed during today's telcon:

1. Powerpoint will be the software that will be used to design the poster
2. Creating samples (containing 10 to 50 entries) of all the 14 tables in the database. -M. Half of this shall be assigned to A.
3. A sample profile of compounds (with 50 records) must be added.
4. Definition of EssoilDB - V and P
5. In the poster, the most unique table in our database should be emphasized upon
6. 10 papers containing the profile of phyto-compounds should be listed. - S and V
7. A story that will represent all the information regarding the selected terpene (from one of the 10 papers) - S and V
8. A sketch of the story (poster) - S

Issues regarding any of these shall be discussed on GitHub as separate issues.

[petermr]

AGENDA 2019-07-10

0. Project management and meeting style

   • times of meetings
   • notice of unavailability
   • forward reports of blockages

1. BRIEF reports from team members (90 secs each). Stand-up style

   • Vinita (Project management and Poster strategy)
   • Shruthi (Narrative)
   • Manish (overview of tables)
   • Ambarish (specific tables and issues)

2. Narrative

   • which papers and plants to select
   • delegation of creation or acquisition of assets (e.g. images, database searches, snippets of text)
   • check papers are in EssoilDB

3. Tables

   • which tables to include in POSTER (EssoilDB2 will have different criteria). We should NOT include tables which are algorithmically derivable from other fields. E.g. plant-family can be deduced from Taxise or Wikidata. It may be useful for speed of searching but this is a second-order problem and of little interest to OpenPlant delegates. We will select from:

     ├── 2.0
     │   ├── EssOilDB Tables.xlsx
     │   ├── essoildb.bibliographydata.csv
     │   ├── essoildb.chemicalgroupdata.csv
     │   ├── essoildb.compoundactivitydata.csv
     │   ├── essoildb.compounddata.csv
     │   ├── essoildb.expconditiondata.csv
     │   ├── essoildb.expmethodologydata.csv
     │   ├── essoildb.infocdata.csv
     │   ├── essoildb.infopdata.csv
     │   ├── essoildb.locationdata.csv
     │   ├── essoildb.plantdata.csv
     │   ├── essoildb.plantfamilydata.csv
     │   ├── essoildb.planthabitdata.csv
     │   ├── essoildb.plantpartdata.csv
     │   └── essoildb.samplecollectiontime.csv
     ├── info_c.csv
     └── info_plant_22122015.csv

     4. Collection of assets for the poster (Vinita) All assets should be on Github and should be open.

[petermr]

Recommended tables for MENTION in poster.

We will need to cut down the number of tables IN THE POSTER. Anything that can be deduced from Wikiadat should be (medicinal activity, weed, family). My guess of the tables we actually need are:

    ├── 2.0
    │   ├── EssOilDB Tables.xlsx
    │   ├── essoildb.bibliographydata.csv
YES, and URGENT (it's empty)
    │   ├── essoildb.chemicalgroupdata.csv
NO - everything is in Wikidata
    │   ├── essoildb.compoundactivitydata.csv
NO - this is not primary data (unless you tell me otherwiise) plants link to Wikidata
    │   ├── essoildb.compounddata.csv
YES and link to Wikidata
    │   ├── essoildb.expconditiondata.csv
YES, needs some normalising
    │   ├── essoildb.expmethodologydata.csv
YES needs normalising
    │   ├── essoildb.infocdata.csv
YES essential , most importat table
    │   ├── essoildb.infopdata.csv
YES essential - the codes need resolving
    │   ├── essoildb.locationdata.csv
YES needs normalising and link to Wikidata
    │   ├── essoildb.plantdata.csv
YES fundamental and link to Wikidata
    │   ├── essoildb.plantfamilydata.csv
NO 
    │   ├── essoildb.planthabitdata.csv
NO this is the "weed" table
    │   ├── essoildb.plantpartdata.csv
YES and link to Wikidata
    │   └── essoildb.samplecollectiontime.csv
YES 
    ├── info_c.csv
    └── info_plant_22122015.csv

[Shruthi-M]

These are the key-points discussed in today's telcon:

1. The data from the article containing the plant from Northeast India will be majorly represented. The related information from other articles will be mentioned in brief.
2. A map which indicates the locations at which this plant is reported.
3. The existence of the papers taken from JEOR in the EssoilDB should be checked.
4. A small paragraph (3-4 sentences) about each table has to be written.
5. The tables and their interlinks should be diagrammatically represented.
6. The table containing data about activity should have the column containing the compound data as well. The column with the heading 'cagroup' should be removed from the compound data table
7. Pictures of the marketed plant product (as a medicine or food), along with their sources
8. The issues regarding bibliography data should be resolved
9. The origin of the information about compound data (Is it from the journals?)

[petermr]

Excellent summary

On Wed, Jul 10, 2019 at 1:03 PM Shruthi-M notifications@github.com wrote:

These are the key-points discussed in today's telcon:

1. The data from the article containing the plant from Northeast India will be majorly represented. The related information from other articles will be mentioned in brief.
2. A map which indicates the locations at which this plant is reported.
3. The existence of the papers taken from JEOR in the EssoilDB should be checked.
4. A small paragraph (3-4 sentences) about each table has to be written.
5. The tables and their interlinks should be diagrammatically represented.
6. The table containing data about activity should have the column containing the compound data as well. The column with the heading 'cagroup' should be removed from the compound data table
7. Pictures of the marketed plant product (as a medicine or food), along with their sources
8. The issues regarding bibliography data should be resolved
9. The origin of the information about compound data (Is it from the journals?)

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[Shruthi-M]

These are some of the points discussed today:

1. There is a need for restructuring of the tables
2. The name 'infopdata' should be replaced by 'profile'
3. In the activity table, multiple activities are grouped under a common id (eg.: 20th entry). This should be looked into.
4. There are some repititions in the file containing methodology data.(eg: 10, 11 and 12).
5. The source file containing approximately 82,000 entries, is not uploaded on GitHub.
6. A complete description of every table along with description of every column in them
7. How many papers in EssoilDB are about O. basilicum?
8. Construction of a story from the different profiles extracted from the papers
9. Snippets of the papers with important parts being highlighted with boxes.

[EmanuelFaria]

Hello all,

I’ve re-constructed the Database Relationship Graph from the files Dr. Gita sent me to clean up, and notice a couple of anomalies (see screenshot attached)

1. I can’t find any place to relate the “caid” in the CompoundActivityData table to any of the others. I assumed it would be found connected to either compounddata or infocdata. Am I missing a table? Or perhaps this field wasn’t exported with what you gave me previously?

2. I find it odd that the only place I can related plantpartdata’s id (ppid) is to infocdata — which otherwise seems to only be related only to things having to do with the compound. … Could this be why the activity percentages were off in the graphs I tried to make from the current database?

Thanks for your help.

Manny

On Jul 11, 2019, at 8:36 AM, Shruthi-M notifications@github.com wrote:

These are some of the points discussed today:

There is a need for restructuring of the tables The name 'infopdata' should be replaced by 'profile' In the activity table, multiple activities are grouped under a common id (eg.: 20th entry). This should be looked into. There are some repititions in the file containing methodology data.(eg: 10, 11 and 12). The source file containing approximately 82,000 entries, is not uploaded on GitHub. A complete description of every table along with description of every column in them How many papers in EssoilDB are about O. basilicum? Construction of a story from the different profiles extracted from the papers Snippets of the papers with important parts being highlighted with boxes. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/gilienv/EssOilDB/issues/51?email_source=notifications&email_token=ACJK2M6C6O2M55GBQL5CIUDP64LKPA5CNFSM4H6VKGKKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZWNNEQ#issuecomment-510449298, or mute the thread https://github.com/notifications/unsubscribe-auth/ACJK2MYMXEBDZ3TIJWR7HV3P64LKPANCNFSM4H6VKGKA.

[Shruthi-M]

Greetings! I have some queries with relation to Lantana and thought of getting them clarified:

1. Lantana camara will be the species we will be presenting.
2. I have to retrieve 5 papers related to this from JEOR.
3. Do these 5 have to be based on the different locations (as previously done with O. basilicum)?
4. Do they have to be in EssoilDB?

[petermr]

Many thanks Shruthi, We are sorry to change direction a bit and hope you haven't done too much already.

On Fri, Jul 12, 2019 at 12:45 PM Shruthi-M notifications@github.com wrote:

Greetings! I have some queries with relation to Lantana and thought of getting them clarified:

1. Lantana camara will be the species we will be presenting.

Yes - this is because it's a key species for NIPGR/GY. The message got a bit lost in all the emails.

1. I have to retrieve 5 papers related to this from JEOR.

Ideally yes. Suggest just Google or otherwise

1. Do these 5 have to be based on the different locations (as previously done with O. basilicum)?

Ideally yes, but not if it's huge amounts of work

1. Do they have to be in EssoilDB?

Ideally, but not essential

P.

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You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/gilienv/EssOilDB/issues/51?email_source=notifications&email_token=AAFTCS5KJA5UL7437PW6XOTP7BVE5A5CNFSM4H6VKGKKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZZQZ7A#issuecomment-510856444, or mute the thread https://github.com/notifications/unsubscribe-auth/AAFTCSY74HKZCGUO5464B3TP7BVE5ANCNFSM4H6VKGKA .

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[Shruthi-M]

Not a problem Sir. I will do my best.

Many thanks Shruthi, We are sorry to change direction a bit and hope you haven't done too much already. On Fri, Jul 12, 2019 at 12:45 PM Shruthi-M @.***> wrote: Greetings! I have some queries with relation to Lantana and thought of getting them clarified:

1. Lantana camara will be the species we will be presenting. Yes - this is because it's a key species for NIPGR/GY. The message got a bit lost in all the emails.
2. I have to retrieve 5 papers related to this from JEOR. Ideally yes. Suggest just Google or otherwise Ok.
3. Do these 5 have to be based on the different locations (as previously done with O. basilicum)? Ideally yes, but not if it's huge amounts of work
4. Do they have to be in EssoilDB? Ideally, but not essential P. — … You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#51?email_source=notifications&email_token=AAFTCS5KJA5UL7437PW6XOTP7BVE5A5CNFSM4H6VKGKKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZZQZ7A#issuecomment-510856444>, or mute the thread https://github.com/notifications/unsubscribe-auth/AAFTCSY74HKZCGUO5464B3TP7BVE5ANCNFSM4H6VKGKA . -- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

[Shruthi-M]

Points discussed today:

• The design of the poster will include tables and pictures.
• Snippets of the profile tables from the selected papers will be included.
• As information regarding habitat and compound activity are derived from secondary sources, they are excluded from the list of tables.
• Chemical pathway showing the role of one of the prominent terpenes along with its role in the invasive characteristic of the species will be included in the poster as a story.
• Other illustrations such as the structure of a terpene, map of Lantana, pictures of the plant and its parts will be added along with the tables.