Errors in annotations - current submissions

[ypriverol]

@qinchunyuan we have found multiple errors in the annotations of the current submissions, please check:

{row: 60, column: "characteristics[disease]"}: "osteosarcoma " contains trailing whitespace {row: 61, column: "characteristics[disease]"}: "osteosarcoma " contains trailing whitespace {row: 62, column: "characteristics[disease]"}: "osteosarcoma " contains trailing whitespace {row: 63, column: "characteristics[disease]"}: "osteosarcoma " contains trailing whitespace {row: 64, column: "characteristics[disease]"}: "osteosarcoma " contains trailing whitespace {row: 65, column: "characteristics[disease]"}: "osteosarcoma " contains trailing whitespace {row: 84, column: "characteristics[disease]"}: "osteosarcoma " contains trailing whitespace {row: 85, column: "characteristics[disease]"}: "osteosarcoma " contains trailing whitespace {row: 86, column: "characteristics[disease]"}: "osteosarcoma " contains trailing whitespace {row: 87, column: "characteristics[disease]"}: "osteosarcoma " contains trailing whitespace {row: 88, column: "characteristics[disease]"}: "osteosarcoma " contains trailing whitespace {row: 89, column: "characteristics[disease]"}: "osteosarcoma " contains trailing whitespace {row: 144, column: "characteristics[disease]"}: "osteosarcoma " contains trailing whitespace {row: 145, column: "characteristics[disease]"}: "osteosarcoma " contains trailing whitespace {row: 146, column: "characteristics[disease]"}: "osteosarcoma " contains trailing whitespace {row: 147, column: "characteristics[disease]"}: "osteosarcoma " contains trailing whitespace {row: 148, column: "characteristics[disease]"}: "osteosarcoma " contains trailing whitespace {row: 149, column: "characteristics[disease]"}: "osteosarcoma " contains trailing whitespace

• [ ] PXD002395 Failed basic validation

The following columns are mandatory and not present in the SDRF: characteristics[cell type], characteristics[age], characteristics[sex] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR The column characteristics[age] is not present in the SDRF -- ERROR The column characteristics[sex] is not present in the SDRF -- ERROR

• [ ] PXD005940 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD004452 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type], characteristics[age], characteristics[sex] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR The column characteristics[age] is not present in the SDRF -- ERROR The column characteristics[sex] is not present in the SDRF -- ERROR

• [ ] PXD005946 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD002087 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD002080 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD012277 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[disease] -- ERROR The column characteristics[disease] is not present in the SDRF -- ERROR {row: 0, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 1, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 2, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 3, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 4, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 5, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 6, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 7, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 8, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 9, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 10, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 11, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 12, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 13, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 14, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 15, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 16, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 17, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 18, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 19, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 20, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 21, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 22, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 23, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 24, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 25, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 26, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 27, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 28, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 29, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 30, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 31, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 32, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 33, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 34, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 35, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 36, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 37, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 38, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 39, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 40, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 41, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 42, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 43, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 44, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 45, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 46, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon {row: 47, column: "characteristics[organism]"}: "mus musculus (mouse)" the term name or title can't be found in the ontology -- ncbitaxon

• [ ] PXD014528 Failed basic validation

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD002081 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD002086 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR -[ ] PXD002088 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD017710 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type], characteristics[age], characteristics[sex] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR The column characteristics[age] is not present in the SDRF -- ERROR The column characteristics[sex] is not present in the SDRF -- ERROR

• [ ] PXD000561 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR -[ ] PXD012255 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[organism part], assay name -- ERROR The column characteristics[organism part] is not present in the SDRF -- ERROR The column assay name is not present in the SDRF -- ERROR {row: 0, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 1, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 2, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 3, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 4, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 5, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 6, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 7, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 8, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 9, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 10, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 11, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 12, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 13, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 14, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 15, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 16, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 17, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 18, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 19, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 20, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 21, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 22, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 23, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 24, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 25, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon {row: 26, column: "characteristics[organism]"}: "yeast" the term name or title can't be found in the ontology -- ncbitaxon -[ ] PXD001819 Failed basic validation

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR {row: 0, column: "characteristics[age]"}: "no available " contains trailing whitespace {row: 1, column: "characteristics[age]"}: "no available " contains trailing whitespace -[ ] PXD018682 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD005355 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR -[ ] PXD011799 Failed validation for human

{row: 0, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 1, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 2, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 3, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 4, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 5, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 6, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 7, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 8, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 9, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 10, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 11, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 12, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 13, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 14, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 15, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 16, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 17, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 18, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon {row: 19, column: "characteristics[organism]"}: "cercopithecus aethiops" the term name or title can't be found in the ontology -- ncbitaxon -[ ] PXD018241 Failed basic validation

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD006512 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD008840 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type], characteristics[age], characteristics[sex] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR The column characteristics[age] is not present in the SDRF -- ERROR The column characteristics[sex] is not present in the SDRF -- ERROR

• [ ] PXD008222 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD005354 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD012755 Failed validation for human

The following columns are mandatory and not present in the SDRF: comment[fraction identifier] -- ERROR The column comment[fraction identifier] is not present in the SDRF -- ERROR

• [ ] PXD005942 Failed basic validation

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD018581 Failed validation for human

The following columns are mandatory and not present in the SDRF: assay name -- ERROR The column assay name is not present in the SDRF -- ERROR

• [ ] PXD003133 Failed basic validation

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD000548 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD002084 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD002619 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type], characteristics[age] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR The column characteristics[age] is not present in the SDRF -- ERROR

• [ ] PXD018117 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD000547 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD002082 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD002049 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type], characteristics[age], characteristics[sex], characteristics[developmental stage] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR The column characteristics[age] is not present in the SDRF -- ERROR The column characteristics[sex] is not present in the SDRF -- ERROR The column characteristics[developmental stage] is not present in the SDRF -- ERROR

• [ ] PXD012203 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD006833 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD012431 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR The column characteristics[developmental stage] is not present in the SDRF -- ERROR

• [ ] PXD010154 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR The column characteristics[developmental stage] is not present in the SDRF -- ERROR

• [ ] PXD000612 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD004682 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type], characteristics[age], characteristics[sex] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR The column characteristics[age] is not present in the SDRF -- ERROR The column characteristics[sex] is not present in the SDRF -- ERROR

• [ ] PXD003668 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD004683 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR -[ ] PXD004684 Failed validation for human

The following columns are mandatory and not present in the SDRF: characteristics[cell type] -- ERROR The column characteristics[cell type] is not present in the SDRF -- ERROR

• [ ] PXD000815 Failed validation for human

[levitsky]

It should be noted that some of the required columns are probably going to be made non-mandatory, pending discussion. It doesn't make sense to add "developmental stage" and "ethnicity" now, as the next version of the validator will have a different set of requirements.

[ypriverol]

I will delete all the projects reports related to developmental stage and ethnicity

[ypriverol]

It should be noted that some of the required columns are probably going to be made non-mandatory, pending discussion. It doesn't make sense to add "developmental stage" and "ethnicity" now, as the next version of the validator will have a different set of requirements.

I'm 100% sure that it would be extremely difficult doing post-annotation to find the ethnicity. I think we should make it optional. what do you think @levitsky

[levitsky]

Like I said in before, I think we should just allow required fields to be "not available", at least in some cases like post-submission annotation. In my opinion that will be necessary in any case.

As for ethnicity (ancestry category), it will probably often be unknown at submission, too. I don't have a strong opinion whether it should or should not be mandatory.

[ypriverol]

@mvaudel do you think we should ask for the ancestry category ethnicity for every submission?