Please add controlled vocabulary

[dlforrister]

Hi, I'm working to upload several plant metabolomics data sets. Can you add the following to the vocabulary?

1) For 'SampleCollectionMethod' please add: "solid material, dried in silica at room temperature"

2) For 'SampleExtractionMethod' please add "water-acetonitrile 60:40"

3) For 'InternalStandardsUsed' please add "biochanin A". Also, have you considered using CAS numbers or some type of identifier that would be analogous to the NCBI taxonomy control? Just a thought to make it more consistent.

4) Can you please add the following species to the NCBITaxonomy:

486047|Inga acuminata 486055|Inga cocleensis 487684|Inga laurina 486059|Inga goldmanii
468147|Inga marginata 486087|Inga thibaudiana 486073|Inga oerstediana 247899|Inga punctata 486071|Inga nobilis 486076|Inga ruiziana 486078|Inga sapindoides 486084|Inga spectabilis 486089|Inga umbellifera 486092|Inga vera 199163|Inga edulis 1620951|Inga cylindrica 1964175|Inga pitmanii 668910|Inga heterophylla 486052|Inga bourgonii 668906|Inga alata 485823|Inga acreana 486082|Inga setosa 668913|Inga venusta 668907|Inga alba 486086|Inga tenuistipula 1954600|Inga lateriflora 670675|Inga fosteriana 670694|Inga suaveolens
[29] 668912|Inga tomentosa 668909|Inga chartacea 670674|Inga coruscans 670676|Inga ingoides
486065|Inga leiocalycina 486050|Inga auristellae 668911|Inga poeppigiana 1620953|Inga grandiflora 1186120|Inga rubiginosa 670671|Inga cayennensis 2793465|Inga glomeriflora 597309|Inga paraensis
688049|Inga gracilifolia 2793475|Inga obidensis 486075|Inga pezizifera 2793483|Inga ulei 1937598|Inga lomatophylla 2793460|Inga brevialata 1937427|Inga splendens 670673|Inga cordatoalata 1186121|Inga stipularis 486085|Inga striata 670672|Inga cinnamomea 1964171|Inga fastuosa 1620952|Inga flagelliformis 597307|Inga huberi 1937597|Inga jenmanii 1736652|Inga longiflora
1186117|Inga longipedunculata 597305|Inga acrocephala 1186118|Inga loubryana 1186119|Inga melinonis
597308|Inga nouragensis 1620954|Inga retinocarpa 1964177|Inga virgultosa 597306|Inga brachystachys 668908|Inga brevipes 486094|Inga vismiifolia 486091|Inga velutina 486081|Inga sertulifera 2793474|Inga multinervis 2793468|Inga kursarii 2793457|Inga aria 2793995|Inga subcapitata 2793473|Inga microcoma 486090|Inga umbratica

5) In addition to the above species we have another 25 species that did not appear in the NCBI Taxonomy and that is because they are new species that have yet to be described and added to NCBI. They are in essence a morphospecies, but we are very confident they are actually species because they are corroborated by traits, morphology, genetics/phylogenies. What would you recommend we do here? Should we do the NCBI for the genus alone and then add a note to the 'SubjectIdentifierAsRecorded' column?

Thank you,

Dale Forrister

[alan-jarmusch]

Hi @dlforrister! thank you for the detailed information. To answer #5 - the options you outline are both okay. You can either add as the genus level (my slight preference) or you can add as the species (in this case the NCBI taxa # would be "not applicable"). Let me know which you prefer and then I'll make all of the updates you requested.

[dlforrister]

Ok, I think we can go with just the genus level but we would like to add a note as to what species they actually are in another column. Is that possible within the SubjectIdentifierAsRecorded or is there another column it makes sense to do this.

The genus would be:

162809 | Inga sp

[alan-jarmusch]

hi @dlforrister sorry for the very slow reply.

I've added all your requested option. The only thing I changed was the solvent system - please use "water-acetonitrile (3:2)" to keep it consistent with the other values.

it's a good idea about the internal standard and adding some identifiers. I'll make a separate note to add something like this. Thanks!

You will have to save a new copy of the template in order to see the options, but you can copy and paste anything you have already entered.

Thanks!