ramonawalls
commented
2 years ago [1] air_PM_concen (air package)
This appears to be a synonym of resp_part_matter (NCBI term) - please clarify if this is a synonym or a new attribute.
respirable particulate matter - concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM
This is a synonym (name change). We request to use the new name. We changed it, because the same term is also used in the food farm environment package.
Note that we now have URI identifiers for terms, which should be adopted for clarity, instead of the structured comment names. I know that will be work for INSDCs, but I hope they can move toward it.
[2] host_sub_specf_gen_lin (host-associated and plant-associated packages)
Does this replace the previous two attributes:
host_infra_specific_name taxonomic information subspecies level host_infra_specific_rank taxonomic rank information below subspecies level, such as variety, form, rank etc.
See issue #73. This was changed so that they host package is consistent with the core terms. Yes, there is only one term now. In hindsight, I think maybe we should have made them both so there are two terms, but it is done now. We can readdress this for MIxS 7 if desired.
[3] water_content (soil package)
NCBI has two attributes: water_content - water content measurement water_content_soil - water content (g/g or cm3/cm3)
Please confirm the soil package should include water_content and NOT water_content_soil. Note that v.6.0 includes the attribute water_cont_soil_meth.
This was part of our effort to harmonize terms across packages. water_content is now one term that is in the soil, sediment, and microbial mat/biofilm packages (MIXS:0000185).
Water content soil method still exists in only the soil package (MIXS:0000323). We should fix that for MIxS 7.
[4] annual_temp (soil package)
NCBI has the attribute annual_season_temp - mean annual and seasonal temperature (oC)
Please confirm if these are synonyms or if annual_temp is a new attribute.
See issue #225. We broke it into two terms, since they are different things.
- annual_temp (MIXS:0000642) is in soil and agriculture
- seasonal_temp (MIXS:0000643) is in soil, food-farm, and agriculture
[5] annual_precpt (soil package)
NCBI has the attribute annual_season_precpt - mean annual and seasonal precipitation (mm)
Please confirm if these are synonyms or if annual_precpt is a new attribute.
Just like temperature, we broke this into two terms:
- annual_precpt (MIXS:0000644) is in soil and agriculture
- seasonal_precpt (MIXS:0000645) is in soil, food-farm, and agriculture
[6] soil_text_measure (soil package)
NCBI has the attribute:
texture - the relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.
Please confirm if these are synonyms or if soil_text_measure is a new attribute.
soil_text_measure (MIXS:0000335) in the soil package is the same as texture (MIXS:0000335) in the soil package in MIxS 5. We changed the label to distinguish it from the other texture terms like wall texture and cell wall texture.
[7] soil_texture_meth (soil package)
NCBI has the attribute:
texture_meth - reference or method used in determining soil texture
Please confirm if these are synonyms or if soil_texture_meth is a new attribute.
soil_texture_method (MIXS:0000336) is a new label for texture_method (MIXS:0000336), to make it clearer.
[8] tot_nitro_content and tot_nitro_cont_meth
NCBI has the following two attributes:
tot_nitro - total nitrogen content of the sample tot_n_method - reference or method used in determining the total N
Please confirm if these are synonyms or new attributes for v6.0. I will request that we rename tot_n_metho to tot_nitro_method.
MIXS 5 had tot_nitro (MIXS:0000102), tot_nitro (MIXS:0000138), tot_nitro_content (MIXS:0000530), tot_nitro_content (MIXS:0000635), tot_nitro_content (MIXS:0000649), tot_nitro_cont_meth (MIXS:0000338), tot_nitro (MIXS:0000681), and tot_nitro (MIXS:0000746).
We consolidated into:
- tot_nitro (MIXS:0000102) (N content in water, in the hydrocarbon, waste water, and water packages)
- tot_nitro_content (MIXS:0000530) (in soil - in the soil and water packages)
- tot_nitro_cont_meth (MIXS:0000338)
If nothing else, this exercise makes is clear why unique IDs for the terms are so important!
tot_nitro_cont_meth (MIXS:0000338)
Hi everyone,
I finally had time to go through the env_packages in v. 6.0 and compared to what we have in BioSample for v. 5.0. I have a few questions - Note that you can view all of the NCBI attributes and definitions here:
https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/
thanks! Anji
*Please also note that for the attributes where the GSC confirms that the v. 6.0 term is a synonym* of an existing NCBI attribute - please indicate which attribute name you would prefer to be displayed in the public view of the BioSample. I will make the request to BioSample but cannot guarantee that they will allow the change. Let me know if you have any questions about this.
[1] air_PM_concen (air package)
This appears to be a synonym of resp_part_matter (NCBI term) - please clarify if this is a synonym or a new attribute.
respirable particulate matter - concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM
[2] host_sub_specf_gen_lin (host-associated and plant-associated packages)
Does this replace the previous two attributes:
host_infra_specific_name taxonomic information subspecies level
host_infra_specific_rank taxonomic rank information below subspecies level, such as variety, form, rank etc.
[3] water_content (soil package)
NCBI has two attributes: water_content - water content measurement water_content_soil - water content (g/g or cm3/cm3)
Please confirm the soil package should include water_content and NOT water_content_soil. Note that v.6.0 includes the attribute water_cont_soil_meth.
[4] annual_temp (soil package)
NCBI has the attribute annual_season_temp - mean annual and seasonal temperature (oC)
Please confirm if these are synonyms or if annual_temp is a new attribute.
[5] annual_precpt (soil package)
NCBI has the attribute annual_season_precpt - mean annual and seasonal precipitation (mm)
Please confirm if these are synonyms or if annual_precpt is a new attribute.
[6] soil_text_measure (soil package)
NCBI has the attribute:
texture - the relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.
Please confirm if these are synonyms or if soil_text_measure is a new attribute.
[7] soil_texture_meth (soil package)
NCBI has the attribute:
texture_meth - reference or method used in determining soil texture
Please confirm if these are synonyms or if soil_texture_meth is a new attribute.
[8] tot_nitro_content and tot_nitro_cont_meth
NCBI has the following two attributes:
tot_nitro - total nitrogen content of the sample tot_n_method - reference or method used in determining the total N
Please confirm if these are synonyms or new attributes for v6.0. I will request that we rename tot_n_metho to tot_nitro_method.