Draft of results - portal overview #26
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Thanks for getting this started. Regarding the following:
I definitely struggled with the description of additional modalities. Technically CITE and multiplexed data are additional sequencing done on the same library or collection of cells vs bulk and spatial which will be a different library. We break down libraries in the table, so I didn't want to gloss over it but I also didn't want to be too confusing?
I recommend trying to take another pass at this when you're addressing the comments I'm returning about Figure 1B, and then I'll try to focus on that as part of my next review.
As mentioned in #46, most of my comments here are around Fig 1A-B, but I also think we should talk more about ontologies to answer your other question.
| All samples on the Portal include a core set of metadata obtained from investigators, including age, sex, diagnosis, subdiagnosis (if applicable), tissue location, and disease stage. | ||
| Some investigators submitted additional metadata, such as treatment and tumor stage also found on the Portal. | ||
| All submitted metadata was standardized as much as possible to maintain consistency across projects before adding to the Portal. | ||
| In addition to providing a human-readable value for the submitted metadata, we also provide an ontology term ID, if applicable. |
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Do we need more information about why it's helpful to have ontologies? Or is stating that we include them enough?
Yes, and it would be helpful to specify which ontologies are used, too, in my opinion. You're underselling the value-add (not to mention the work that went into the metadata) the way this is currently written.
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Reading the first methods PR reminded me that we should probably file an issue to track methods for the ontologies!
content/03.results.md
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| However, some samples include additional data, such as quantified data from tagging cells with Antibody-derived tags (ADT), like CITE-seq[@doi:10.1038/nmeth.4380], or multiplexing samples with hashtag oligonucleotides (HTO)[@doi:10.1186/s13059-018-1603-1]. | ||
| In some cases, multiple libraries from the same sample were collected to conduct either bulk RNA-seq or spatial transcriptomics. | ||
| Downloading a sample on the Portal will include sequencing data from all associated libraries, including data from any additional modalities mentioned here. | ||
| A summary of the number of samples with each additional modality is shown in Figure 1B, and a detailed summary of the total samples with each sequencing method broken-down by project, is available in Supplemental Table 1. |
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Similar to the comment above, how you're talking about the figure in the main text should add additional benefits for the audience, not just summarize the legend. For example, what proportion of samples in the Portal have an additional modality?
…lts-edits Add JNT edits to overview section of results
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Click the link below to download the manuscript build as a ZIP file. |
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Click the link below to download the manuscript build as a ZIP file. |
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I made the following changes:
You made this comment in #46:
Does this mean we should remove the project card information? What description of downloads are you specifically referring to? @jaclyn-taroni this should be ready for another look. |
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Click the link below to download the manuscript build as a ZIP file. |
I took the description of what downloads are available out: https://github.com/AlexsLemonade/ScPCA-manuscript/pull/46/files#diff-79bf22740443da98b87b364ef8ccd6495aa7c14b98b8e5354d7c38bd66e4af71L25 |
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Click the link below to download the manuscript build as a ZIP file. |
content/03.results.md
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| Some investigators submitted additional metadata, such as treatment and tumor stage, which can also be found on the Portal. | ||
| All submitted metadata was standardized to maintain consistency across projects before adding to the Portal. | ||
| In addition to providing a human-readable value for the submitted metadata, we also provide an ontology term ID, if applicable. | ||
| We mapped submitted metadata for age, sex, organism, disease, tissue, and ethnicity (if applicable), to their associated ontology term IDs using the ontology lookup service. |
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This does not fully address my comment (https://github.com/AlexsLemonade/ScPCA-manuscript/pull/26/files#r1501617420):
Yes, and it would be helpful to specify which ontologies are used, too, in my opinion.
I meant the ontologies themselves. So, UBERON, MONDO, etc. If you want to add a TODO in an HTML comment and let others weigh in later, that would be fine. I expect that #50 would include this level of detail.
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Sorry, I wasn't sure how much detail to go into here vs. the methods regarding the names of the actual ontologies. I updated this to indicate both where the ontology comes from and what metadata they are used for in d76f191 if you want to take another look.
Co-authored-by: Jaclyn Taroni <[email protected]>
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Click the link below to download the manuscript build as a ZIP file. |
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Click the link below to download the manuscript build as a ZIP file. |
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Click the link below to download the manuscript build as a ZIP file. |
content/03.results.md
Outdated
| Some investigators submitted additional metadata, such as treatment and tumor stage, which can also be found on the Portal. | ||
| All submitted metadata was standardized to maintain consistency across projects before adding to the Portal. | ||
| In addition to providing a human-readable value for the submitted metadata, we also provide an ontology term ID, if applicable. | ||
| Submitted metadata was mapped to an associated ontology term IDs obtained from HsapDV (age), PATO (sex), NCBI taxonomy (organism), MONDO (disease), UBERON (tissue), and Hancestro (ethnicity, if applicable). |
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I'd add citations, but LGTM otherwise
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Click the link below to download the manuscript build as a ZIP file. |
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Click the link below to download the manuscript build as a ZIP file. |
This PR includes a draft of the first section in the results. I mostly followed the outline that we had written.